Fragment mode analysis and its application to the vibrational normal modes of boron trichloride-ammonia and boron trichloride-pyridine complexes

A method for expressing quantitatively the vibrational normal modes of a molecule in a basis set consisting of the normal vibrations (plus translations and rotations) of its constituent fragments is presented. The method is illustrated by describing the vibrational modes of BCl3-NH3 and BCl3-pyridine electron donor-acceptor complexes in terms of motions of BCl3 and either NH3 or pyridine. These complexes show examples of mixing between modes located on different fragments, mixing between modes of one fragment due to symmetry lowering, and the transformation of six fragment translations/rotations into vibrations of the complex. Although perturbation theory has been proposed to explain such examples of mode mixing, calculations imply that interactions between fragments of both complexes are too strong for perturbation theory to be generally applicable. In addition, the transformation of fragment rotations and/or translations into vibrations of the composite molecule will always occur and cannot be understood in detail by using perturbation theory. For the BCl3-pyridine complex, a band observed at 1107 cm(-1) is re-assigned as a combination of C-H in-plane bending and a ring-breathing mode of the pyridine fragment.     

Repeat space theory applied to carbon nanotubes and related molecular networks. III

The present article is part III of a series devoted to extending the Repeat Space Theory (RST) to apply to carbon nanotubes and related molecular networks. In this part III, four problems concerning the above-mentioned extension of the RST have been formulated. Affirmative solutions of these problems imply (i) asymptotic analysis of carbon nanotubes (CNTs) via the new techniques of normed repeat space, Banach algebra, and C*-algebra becomes possible; (ii) a new linkage is formed between the investigations of CNTs and those of ‘spectral symmetry’. In the present paper, we give affirmative solutions to all of the four problems, together with (a) estimates of the norms of matrix sequences representing CNTs, (b) Challenging Problem A^#, which complements Problems A, (c) several pictures of ‘CNT Matrix Art’ which has heuristic power to lead one to get the affirmative answers to the problems formulated in an abstract algebraic manner.     

Correlations Between Amino Acids at Different Sites in Local Sequences of Protein Fragments with Given Structural Patterns

Ample evidence suggests that the local structures of peptide fragments in native proteins are to some extent encoded by their local sequences. Detecting such local correlations is important but it is still an open question what would be the most appropriate method. This is partly because conventional sequence analyses treat amino acid preferences at each site of a protein sequence independently, while it is often the inter-site interactions that bring about local sequence-structure correlations. Here a new scheme is introduced to capture the correlation between amino acid preferences at different sites for different local structure types. A library of nine-residue fragments is constructed, and the fragments are divided into clusters based on their local structures. For each local structure cluster or type, chi-square tests are used to identify correlated preferences of amino acid combinations at pairs of sites. A score function is constructed including both the single site amino acid preferences and the dual-site amino acid combination preferences, which can be used to identify whether a sequence fragment would have a strong tendency to form a particular local structure in native proteins. The results show that, given a local structure pattern, dual-site amino acid combinations contain different information from single site amino acid preferences. Representative examples show that many of the statistically identified correlations agree with previously-proposed heuristic rules about local sequence-structure correlations, or are consistent with physical-chemical interactions required to stabilize particular local structures. Results also show that such dual-site correlations in the score function significantly improves the Z-score matching a sequence fragment to its native local structure relative to nonnative local structures, and certain local structure types are highly predictable from the local sequence alone if inter-site correlations are considered.     

AlnO2±团簇结构的几何特征与稳定性

采用密度泛函理论(DFT)的B3LYP方法,在6-311G**水平上对AlnO2±(n=1-10)团簇的几何和电子结构进行了理论计算.讨论了混合团簇的基态结构与振动频率,以及电荷转移与分子轨道.结果表明,AlnO2±(n>1)团簇的基态结构都是2个较小的AlmO(m相似文献   

Validity and validation of expert (Q)SAR systems

At a recent workshop in Setubal (Portugal) principles were drafted to assess the suitability of (quantitative) structure–activity relationships ((Q)SARs) for assessing the hazards and risks of chemicals. In the present study we applied some of the Setubal principles to test the validity of three (Q)SAR expert systems and validate the results. These principles include a mechanistic basis, the availability of a training set and validation. ECOSAR, BIOWIN and DEREK for Windows have a mechanistic or empirical basis. ECOSAR has a training set for each QSAR. For half of the structural fragments the number of chemicals in the training set is >4. Based on structural fragments and log Kow, ECOSAR uses linear regression to predict ecotoxicity. Validating ECOSAR for three ‘valid’ classes results in predictivity of ?≥?64%. BIOWIN uses (non-)linear regressions to predict the probability of biodegradability based on fragments and molecular weight. It has a large training set and predicts non-ready biodegradability well. DEREK for Windows predictions are supported by a mechanistic rationale and literature references. The structural alerts in this program have been developed with a training set of positive and negative toxicity data. However, to support the prediction only a limited number of chemicals in the training set is presented to the user. DEREK for Windows predicts effects by ‘if-then’ reasoning. The program predicts best for mutagenicity and carcinogenicity. Each structural fragment in ECOSAR and DEREK for Windows needs to be evaluated and validated separately.     

Generalized energy-based fragmentation approach for computing the ground-state energies and properties of large molecules

We present a generalized energy-based fragmentation (GEBF) approach for approximately predicting the ground-state energies and molecular properties of large molecules, especially those charged and polar molecules. In this approach, the total energy (or properties) of a large molecule can be approximately obtained from energy (or properties) calculations on various small subsystems, each of which is constructed to contain a certain fragment and its local surroundings within a given distance. In the quantum chemistry calculation of a given subsystem, those distant atoms (outside this subsystem) are modeled as background point charges at the corresponding nuclear centers. This treatment allows long-range electrostatic interaction and polarization effects between distant fragments to be taken into account approximately, which are very important for polar and charged molecules. We also propose a new fragmentation scheme for constructing subsystems. Our test calculations at the Hartree-Fock and second-order M?ller-Plesser perturbation theory levels demonstrate that the approach could yield satisfactory ground-state energies, the dipole moments, and static polarizabilities for polar and charged molecules such as water clusters and proteins.     

Front Cover: High-level ab initio evidence of bipyramidal Cu5 clusters as fluxional Jahn-Teller molecules (ChemPhysChem 19/2023)

Novel highly selective synthesis techniques have enable the production of atomically precise monodisperse metal clusters (AMCs) of subnanometer size. These AMCs exhibit ‘molecule-like’ structures that have distinct physical and chemical properties, significantly different from those of nanoparticles and bulk material. In this work, we study copper pentamer Cu₅ clusters as model AMCs by applying both density functional theory (DFT) and high-level (wave-function-based) ab initio methods, including those which are capable of accounting for the multi-state multi-reference character of the wavefunction at the conical intersection (CI) between different electronic states and augmenting the electronic basis set till achieving well-converged energy values and structures. After assessing the accuracy of a high-level multi-multireference ab initio protocol for the well-known Cu₃ case, we apply it to demonstrate that bypiramidal Cu₅ clusters are distorted Jahn-Teller (JT) molecules. The method is further used to evaluate the accuracy of single-reference approaches, finding that the coupled cluster singles and doubles and perturbative triples CCSD(T) method delivers the results closer to our ab initio predictions and that dispersion-corrected DFT can outperform the CCSD method. Finally, we discuss how JT effects and, more generally, conical intersections, are intimately connected to the fluxionality of AMCs, giving them a ‘floppy’ character that ultimately facilitates their interaction with environmental molecules and thus enhances their functioning as catalysts.     

(CoCr)n (n=1-5)合金团簇的结构和磁性

采用密度泛函理论中的广义梯度近似(GGA)对(CoCr)n (n=1-5)团簇的几何结构、电子结构和磁性进行了系统的研究, 确定了团簇的基态和亚稳态. 结果表明, CoCr二元合金团簇的基态几何构型呈对称有序排列, 其磁性均呈反铁磁性耦合; 团簇键长和配位数的大小对原子局域磁性有很明显的影响; 受Cr原子的影响, 在(CoCr)4团簇中, 非相邻的Co原子之间呈现反铁磁性耦合.     

Density functional calculation of transition metal cluster energy surfaces

A quantum field mechanics of an electron subsystem in 3D physical space as the topology of compact atomic clusters with spontaneously broken local canonical symmetry is used for investigation of different types of microdefects in the condensed state of transition metals. The theory is illustrated with results of calculation of small compact Fe_n clusters (n = 2, 6, 14).     

Structure of silver clusters with magic numbers of atoms by data of molecular dynamics

The behavior of silver clusters (cubic octahedron habit) with magic numbers of atoms N = 13, 55, 146, 309, 561, 923, 1415, and 2057 in the 0–1300 K temperature range is studied for the embeded atom model by the molecular dynamics method. The structural method for the analysis of the dynamics of local configurations of atoms based on the construction of angular characteristics of simplexes of the Delone partition of a cluster is proposed. Structural transitions of clusters with a cubic octahedron habit to the stable clusters with an icosahedron habit are revealed. Motions of atoms in clusters with an icosahedron habit are transformed into the stationary vibration mode. Middle positions of atoms in clusters tend to form shells with a regular structure. At N = 561, there are 15 such shells. The cluster with N = 561 at 650 K is characterized by a reduced density close to that of silver melt.     

Matrix suppression and analyte suppression effects of quaternary ammonium salts in matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry: an investigation of suppression mechanism

In the matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI TOF MS) analysis of some quaternary ammonium salts (QASs), very clean spectra of the quaternary ammonium ions were recorded with a strong matrix suppression effect (MSE). The QASs also showed a considerable analyte suppression effect (ASE). It was demonstrated that the MSE and ASE of the QASs can be explained well by the cluster ionization model. According to this model, MALDI ions are formed from charged matrix/analyte clusters. Various analyte ions and matrix ions might coexist in the cluster, and they will compete for the limited number of net charges available. If enough quaternary ammonium ions are present in the cluster, they will take away the net charges, thus resulting in the MSE and ASE. Our results also suggest that ‘the cluster ionization model’ is not in conflict with ‘the theory of ionization via secondary gas‐phase reactions’. The initial MALDI ions produced from charged matrix/analyte clusters will collide with other molecules or ions in the MALDI plume. Depending on the properties of the initial ions and the composition of the MALDI plume, secondary gas‐phase reactions might result from these collisions. The final ions observed are the combined results of ‘cluster ionization’ and ‘ionization via secondary gas‐phase reactions’. Copyright © 2009 John Wiley & Sons, Ltd.     

B2Cn+(n=1～9)团簇的结构及其稳定性

采用密度泛函理论(DFT)的B3LYP泛函, 在6-311G*水平上对B2Cn+(n=1～9)团簇的几何构型和电子结构进行了优化和振动频率计算. 结果表明, 在B2Cn+(n=1～9)团簇的基态构型中, B2C2+、B2C3+为具有D∞h对称性的线形结构, B2C7+为具有Cs对称性的立体环状结构, 其余均为平面构型; 其成键顺序为C—C成键优于B—C 成键, B—C成键优于B—B成键. 进一步得到了B2Cn+(n=1～9)团簇的总能量(ET)、零点能(EZ)、摩尔热容(Cp)、标准熵(S0)以及原子化能(ΔEn+). 其结果显示, 随着n的递增, ET、EZ、Cp、S0和ΔEn+数值均呈现增大趋势, 其中EZ数值呈现近似等梯度的增加趋势. 通过对B2Cn+(n=1～9)团簇基态结构的垂直电子亲合势的研究发现, n为奇数的B2Cn+团簇比n为偶数的稳定.     

Molecules and crystals with both icosahedral and cubic symmetry

Notwithstanding the apparent incompatibility between octahedral and icosahedral symmetries, fragments with the two types of symmetry coexist in many molecules and crystals, as evidenced by continuous shape and symmetry measures. A geometric analysis of Platonic and Archimedean polyhedra and of a variety of molecular and crystal structures strongly suggests that octahedral symmetry is latent in icosahedral polyhedra and vice versa. In this Feature Article, new concepts and structural data from the literature combine to offer a perspective view of complex molecular and extended structures. Its influence on the common cubic packing of icosahedral molecules is discussed for a variety of examples, including water clathrates, dodecahedrane, Buckminsterfullerene, the Pd145 and Mo132 clusters and several intermetallic phases.     

Local-MP2 electron correlation method for nonconducting crystals

Rigorous methods for the post-HF (HF-Hartree-Fock) determination of correlation corrections for crystalline solids are currently being developed following different strategies. The CRYSTAL program developed in Torino and Daresbury provides accurate HF solutions for periodic systems in a basis set of Gaussian type functions; for insulators, the occupied HF manifold can be represented as an antisymmetrized product of well localized Wannier functions. This makes possible the extension to nonconducting crystals of local correlation linear scaling On techniques as successfully and efficiently implemented in Stuttgart's MOLPRO program. These methods exploit the fact that dynamic electron correlation effects between remote parts of a molecule (manifesting as dispersive interactions in intermolecular perturbation theory) decay as an inverse sixth power of the distance R between these fragments, that is, much more quickly than the Coulomb interactions that are treated already at the HF level. Translational symmetry then permits the crystalline problem to be reduced to one concerning a cluster around the reference zero cell. A periodic local correlation program (CRYSCOR) has been prepared along these lines, limited for the moment to the solution of second-order Moller-Plesset equations. Exploitation of point group symmetry is shown to be more important and useful than in the molecular case. The computational strategy adopted and preliminary results concerning five semiconductors with tetrahedral structure (C, Si, SiC, BN, and BeS) are presented and discussed.     

Orbital Correspondence Analysis in Maximum Symmetry

A method is described in which the ‘allowed’ course of a reaction is determined by means of an analysis – within the symmetry point group common to reactants and products – of their molecular orbitals and of the distortions that occur along the reaction path connecting them. The procedure, and its relation to and advantages over conventional correlation methods, is illustrated with a few very well known reactions: Cyclization of hexatriene, the ‘photochemical Diels-Alder reaction’ and the stepwise and concerted [2+2]-cycloadditions.     

Embedded,graph-theoretically defined many-body approximations for wavefunction-in-DFT and DFT-in-DFT: Applications to gas- and condensed-phase ab initio molecular dynamics,and potential surfaces for quantum nuclear effects

We present a graph-theoretic approach to adaptively compute many-body approximations in an efficient manner to perform (a) accurate post-Hartree–Fock (HF) ab initio molecular dynamics (AIMD) at density functional theory (DFT) cost for medium- to large-sized molecular clusters, (b) hybrid DFT electronic structure calculations for condensed-phase simulations at the cost of pure density functionals, (c) reduced-cost on-the-fly basis extrapolation for gas-phase AIMD and condensed phase studies, and (d) accurate post-HF-level potential energy surfaces at DFT cost for quantum nuclear effects. The salient features of our approach are ONIOM-like in that (a) the full system (cluster or condensed phase) calculation is performed at a lower level of theory (pure DFT for condensed phase or hybrid DFT for molecular systems), and (b) this approximation is improved through a correction term that captures all many-body interactions up to any given order within a higher level of theory (hybrid DFT for condensed phase; CCSD or MP2 for cluster), combined through graph-theoretic methods. Specifically, a region of chemical interest is coarse-grained into a set of nodes and these nodes are then connected to form edges based on a given definition of local envelope (or threshold) of interactions. The nodes and edges together define a graph, which forms the basis for developing the many-body expansion. The methods are demonstrated through (a) ab initio dynamics studies on protonated water clusters and polypeptide fragments, (b) potential energy surface calculations on one-dimensional water chains such as those found in ion channels, and (c) conformational stabilization and lattice energy studies on homogeneous and heterogeneous surfaces of water with organic adsorbates using two-dimensional periodic boundary conditions.     

Multireference coupled-cluster study of the symmetry breaking in the C2B radical

The potential energy surfaces (PESs) for both the ground and the excited electronic states of the C(2)B radical are investigated using various multireference (MR) coupled-cluster (CC) approaches. In the ground state case we employ the reduced MR (RMR) CC approach with singles (S) and doubles (D), the RMR CCSD method, as well as its RMR CCSD(T) version corrected for secondary triples, relying on various model spaces and basis sets. The reliability of this approach is also tested against the benchmark full configuration interaction results obtained for a small Dunning-Hay (DH) basis set. The results imply a clear preference for a cyclic structure which, however, breaks the C(2v) symmetry. This symmetry breaking manifests itself strongly at the level of the independent particle model, as represented by the restricted open-shell Hartree-Fock approximation, but the tendency toward symmetry breaking diminishes with the increasing size of the basis set employed as well as with the enhanced account of the correlation effects. It is likely to disappear in the complete basis set limit. The general model space CCSD method is then used to compute vertical excitation energies for a number of excited states as well as the cuts of the PES as the boron atom moves around the C(2) fragment. These results also explain why no symmetry breaking is found when relying on a spin contaminated unrestricted Hartree-Fock reference, as in the UMP2 method.