A concurrent algorithm for parallel calculation of eigenvalues and eigenvectors of real symmetric matrices

Elementary Jacobi Rotations are used as the basic tools to obtain eigenvalues and eigenvectors of arbitrary real symmetric matrices. The proposed algorithm has a complete concurrent structure, that is: every eigenvalue-eigenvector pair can be obtained in any order and in an independent way from the rest. Examples based on diagonally dominant real symmetric matrices are given.     

A graph-theoretical method for stepwise factorisation of symmetric graphs for simultaneous determination of eigenvectors and eigenvalues

A simple pictorial algorithm for factorisation of symmetric chemical graphs (weighted and unweighted) leading to simultaneous determination of their eigenvalues and eigenvectors has been devised. The method does not require group-theoretical techniques (viz. identification of the point group of the species under study, formation of symmetryadopted linear combinations using character tables etc.). It requires consideration of only one symmetry element, e.g., a reflection plane and is based on elementary row and column operations which keep the secular determinant of the adjacency matrix unchanged (except possibly for a multiplicative constant).     

Entanglement and Energy for Vibrationally Localized States in Molecule CS2

The dynamics of quantum entanglement described by the von Neumann entropy is studied for the localized states of Fermi-resonance coupling vibrations in molecule CS₂, where the interacting energy between the stretching and the bending modes is considered to establish a connection between entanglement and energy. It is shown that entanglement reveals dominant anti-correlation with the interacting energy for the stretch-localized state, while that exhibits dominantly positive correlation for the bend-localized state. The entanglement and the energy for the dislocalized states are discussed as well. Those are useful for molecular quantum computing and quantum information in high dimensional states.     

Fidelity and Mutual Entropy in Mixed States for Fermi-resonance Coupling Vibrations of CS2

states of Fermi-resonance coupling vibrations in molecule CS₂. It is demonstrated that those fidelities are dominant-positively correlated with each other, one of which by Wang et al. (Phys. Lett. A 373, 58 (2008)) is the most striking in dominant anti-correlation with quantum mutual entropy. That is useful for molecular quantum computing and quantum information.     

The IINS/quantum chemical studies of 17α- and 21-hydroxy-derivatives of progesterone

The inelastic incoherent neutron scattering and quantum chemical studies have been performed on 17 and 21 hydroxy progesterone and the assignment of internal modes have been proposed in the range up to 700 cm⁻¹. The lattice branch of PDS reveals modes which could be attributed to torsions of rings A and D (cyclohexane and cyclopentane) of the pregnane skeleton. An assignment of the torsional vibrations of methyl groups in the range 150–300 cm⁻¹ and the deformation and out-of plane vibrations of CCOH groups has been proposed. An analysis of the effect of hydrogen bonds on PDS spectra has been performed.     

Extensions and tests of “multimode”: a code to obtain accurate vibration/rotation energies of many-mode molecules

We describe extensions and tests of the code “multimode” which does vibrational self-consistent field method (VSCF) and two types of state-mixing (denoted VSCF-CI and V-CI) for rovibrational energies of many-mode systems. The extensions include an exact treatment of rotation, flexible approaches to perform the CI calculations, and the inclusion of a Davidson diagonalization routine to find low-lying eigenvalues of large matrices. The code is tested against previous exact variational calculations for non-rotating H₂CN, and J=0 and J=1 rovibrational states of H₂CS. The code represents the full potential by a hierarchical n-mode representation, where n is the number of normal coordinates that are coupled together. Tests are presented for the convergence and accuracy of this representation for n equal to 3 and 4, where 4 is the current maximum value. These tests are done at the VSCF and V-CI level, with very encouraging results. Received: 8 June 1998 / Accepted: 11 August 1998 / Published online: 19 October 1998     

A multiconfigurational SCF computational method for the resolution of the vibrational Schrödinger equation in polyatomic molecules

Summary A new variational method for solving the molecular vibration problem is proposed. The so-called VMCSCF method (vibrational multiconfigurational self-consistent field) is based on the super-CI algorithm, previously developed in the framework of electronicab initio calculations. This approach makes direct use of the generalised Brillouin theorem to ensure self-consistency. The method is dedicated to the study of strongly interacting states (vibrational resonances), which are one of the main sources of perturbation in vibrational spectra. The interest of the method to tackle resonance interactions is illustrated by means of test calculations performed on the water and formaldehyde molecules.     

A new method for assigning the CO stretching bands in cis-disubstituted octahedral metal carbonyl complexes

The paper describes a method for assigning the CO stretching bands in cis-disubstituted metal carbonyls of the types L₂M(CO)₄, (LL)M(CO)₄, LL′M(CO)₄ and (LL′)M(CO)₄. The method was based on the parameter δ, defined as δ=(λ₁−λ₂)/(λ₁+λ₂−2λ₄) where λ₁, λ₂ and λ₄ are the λ parameters of the a₁⁽¹⁾, a₁⁽²⁾ and b₂ modes, respectively. For a large number of complexes with the above general formulas, the average value of δ was found to be 0.62, with a standard deviation of 0.02. It was shown that this range of δ can be used as a criterion of the correct band assignment for the complexes understudy.     

New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates

A new algorithm for parallel calculation of the second derivatives (Hessian) of the conformational energy function of biomolecules in internal coordinates is proposed. The basic scheme of this algorithm is the division of the entire calculation of the Hessian matrix (called "task") into subtasks and the optimization of the assignment of processors to each subtask by considering both the load balancing and reduction of the communication cost. A genetic algorithm is used for this optimization considering the dependencies between subtasks. We applied this method to a glutaminyl transfer RNA (Gln-tRNA) molecule for which the scalability of our previously developed parallel algorithm was significantly decreased when the large number of processors was used. The speedup for the calculation was 32.6 times with 60 processors, which is considerably better than the speedup for our previously reported parallel algorithm. The elapsed time for the calculation of subtasks, data sending, and data receiving was analyzed, and the effect of the optimization using the genetic algorithm is discussed.     

振动和转动激发对N2在Fe(111)表面解离吸附的影响(英文)

N₂的解离化学吸附是工业合成氨的速控步骤.基于最近构建的六维势能面,本文研究了N₂的初始振动激发和转动激发在Fe(111)表面的反应性的作用.由于该反应具有重要的量子效应,通过六维量子动力学计算研究了入射能量低于1.6 eV时振动激发的效应.并采用准经典轨线计算揭示了高入射能量下的振动和转动激发的影响.通过这些研究发现增加平动能量在一定程度上能提高解离几率,振动激发或转动激发能更有效地促进解离.这项研究为重原子分子-表面反应的模式特异性动力学提供了有价值的见解.     

Accurate energy eigenvalues and eigenfunctions for the two‐dimensional confined hydrogen atom

A study of the two‐dimensional hydrogen atom confined within a circle of impenetrable walls is presented. The potential inside the box is Coulomb type, whereas outside it is infinite. The energy eigenvalues and some radial wave function properties are computed with high accuracy for different box sizes. We derive the polarizability in the Kirkwood approximation, calculate the Fermi contact term as a function of the confinement radius, and investigate the filling order of the one‐electron states. When the electronic configuration of many electrons is constructed by means of the Aufbau principle, the model predicts the inversion 2s–3d levels in the N atom. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

A facile method to prepare CdS/polystyrene composite particles

Nano-CdS/polystyrene composite particles were prepared via surfactant-free emulsion polymerization. 2-(Dimethylamino)ethyl methacrylate (DMEMA) was used as auxiliary monomer which co-polymerized with styrene (St) and provided the location for coordinating with Cd²⁺. By the coordination of Cd²⁺ ions to DMEMA, mono-disperse polystyrene with the Cd²⁺ ions on the particles surface were prepared successfully. With the release of S²⁻ ions from the thioacetamide (TAA), cadmium sulfide (CdS) was formed. Nano-CdS/PS composite particles could be synthesized via this facile method. The order of materials addition and the amount of initiator both are playing important roles to the final morphologies of the composite particles. In the method proposed in this study, no surfactant was used, and the stable emulsion was successfully obtained. UV–vis absorption and fluorescence measurement indicated the quantum dot effect in the resulted nano-CdS/PS composite particles. The possible composite particle formation mechanism was presented.     

Gas-phase synthesis and characterization of heteroleptic divalent germanium compounds by FVT/UV-PES

The flash vacuum thermolysis/UV photoelectron spectroscopic (FVT/UV-PES) technique has been applied for the synthesis of three cyclic germanediyls containing oxo-thio, oxo-amino, and thio-amino substitution at germanium. The three compounds (4b, 5b and 6b) were prepared from the corresponding 3,4-dimethyl-1-germacyclopent-3-enes (4a, 5a and 6a) by thermal cheletropic elimination, and the photoelectron spectra of both sets of molecules were measured. The course of the thermolysis reactions has also been confirmed by mass spectrometric methods and the results of chemical trapping experiments. The assignment of the PE spectral bands for the two series of molecules has been carried out with the aid of time dependent DFT (TD-DFT) and outer valence green’s function (OVGF) calculations. The results indicate that the strong σ-withdrawing effect of oxygen and the strong π-donating effect of nitrogen are the two main factors affecting the electronic structures of these germylene derivatives.     

Binding energies of tyrosine kinase inhibitors: Error assessment of computational methods for imatinib and nilotinib binding

The binding energies of imatinib and nilotinib to tyrosine kinase have been determined by quantum mechanical (QM) computations, and compared with literature binding energy studies using molecular mechanics (MM). The potential errors in the computational methods include these critical factors:

• •Errors in X-ray structures such as structural distortions and steric clashes give unrealistically high van der Waals energies, and erroneous binding energies.
• •MM optimization gives a very different configuration to the QM optimization for nilotinib, whereas the imatinib ion gives similar configurations
• •Solvation energies are a major component of the overall binding energy. The QM based solvent model (PCM/SMD) gives different values from those used in the implicit PBSA solvent MM models. A major error in inhibitor—kinase binding lies in the non-polar solvation terms.
• •Solvent transfer free energies and the required empirical solvent accessible surface area factors for nilotinib and imatinib ion to give the transfer free energies have been reverse calculated. These values differ from those used in the MM PBSA studies.
• •An intertwined desolvation—conformational binding selectivity process is a balance of thermodynamic desolvation and intramolecular conformational kinetic control.
• •The configurational entropies (TΔS) are minor error sources.

     

CdSe/CdS量子点荧光猝灭法测定芹黄素的研究

以巯基乙酸为稳定剂,在水溶液中合成了具有特殊光学性质的水溶性CdSe/CdS量子点。以该量子点为荧光探针,基于荧光猝灭法对芹黄素进行了定量检测。考察了缓冲体系、反应时间、量子点浓度等多种因素的影响。实验结果表明,在0.001 mol/L、pH为6.80的KH2PO4-Na2HPO4缓冲液中,当量子点浓度为1.2×10^-4mol/L、反应时间为20 min时,该方法的线性范围为0.16-27.02μg/mL,其线性回归方程为F0/F=0.99665＋0.11067ρ（μg/mL）,相关系数r=0.998,检出限为0.13μg/mL,并用于合成样品的分析。     

A new method for the detection of ATP using a quantum-dot-tagged aptamer

Fluorescence resonance energy transfer (FRET) between a quantum dot as donor and an organic fluorophore as acceptor has been widely used for detection of nucleic acids and proteins. In this paper, we developed a new method, characterized by 605-nm quantum dot (605QD) fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease, to detect adenosine triphosphate (ATP). The new method involved the use of three different oligonucleotides: 3′-biotin-modified DNA that binds to streptavidin-conjugated 605QD; 3′-Cy5-labelled DNA; and a capture DNA consisting of an ATP aptamer and a sequence which could hybridize with both 3′-biotin-modified DNA and 3′-Cy5-labelled DNA. In the absence of the target ATP, the capture DNA binds to 3′-biotin-modified DNA and 3′-Cy5-labelled DNA, bringing quantum dot and Cy5 into close proximity for greater FRET efficiency. When ATP is introduced, the release of the 3′-Cy5-labelled DNA from the hybridization complex took place, triggering 605QD fluorescence intensity increase and corresponding Cy5 fluorescence intensity decrease. Taken together, the virtue of FRET pair 605QD/Cy5 and the property of aptamer-specific conformation change caused by aptamer–ATP interaction, combined with the fluorescence intensity change of both 605QD and Cy5, provide prerequisites for simple and convenient ATP detection. Zhang Chen and Guang Li contributed equally to this work.     

A highly efficient capillary electrophoresis-based method for size determination of water-soluble CdSe/ZnS core-shell quantum dots

This paper describes a highly efficient method for size determination of water-soluble CdSe/ZnS core-shell quantum dots (QDs) by capillary electrophoresis (CE) using polymer additive as sieving medium. The influence of some factors, such as kinds and concentrations of the sieving medium, pH, concentrations of the background electrolyte (BGE) and applied voltage, on the separation of QDs was investigated. Under the optimal separation conditions, four different sized QDs were successfully separated, and the relative standard deviation (RSD) of the migration times for these QDs was below 1.013%. In addition, an equation was fit by taking into account the correlation existing between the electrophoretic mobilities and the sizes of a set of QDs. The feasibility of this equation to measure the sizes of other QDs was confirmed by comparison with the sizes obtained by transmission electron microscopy (TEM) experiment. This work offers a novel method for size determination of QDs, and provides an important reference on the study of QDs based on CE.     

Methods for parallel computation of SCF NMR chemical shifts by GIAO method: Efficient integral calculation,multi-Fock algorithm,and pseudodiagonalization

We implemented our gauge-including atomic orbital (GIAO) NMR chemical shielding program on a workstation cluster, using the parallel virtual machine (PVM) message-passing system. On a modest number of nodes, we achieved close to linear speedup. This program is characterized by several novel features. It uses the new integral program of Wolinski that calculates integrals in vectorized batches, increases efficiency, and simplifies parallelization. The self-consistent field (SCF) step includes a multi-Fock algorithm, i.e., the simultaneous calculation of several Fock matrices with the same integral set, increasing the efficiency of the direct SCF procedure. The SCF diagonalization step, which is difficult to parallelize, has been replaced by pseudodiagonalization. The latter, widely used in semiempirical programs, becomes important in ab initio type calculations above a certain size, because the ultimate scaling of the diagonalization step is steeper than that of integral computation. Examples of the calculation of the NMR shieldings in large systems at the SCF level are shown. Parallelization of the density functional code is underway. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 816–825, 1997