On the use of projection operators in molecular dynamics

Symmetry coordinates are easily constructed when operating in mass-weighted Cartesian space. Such coordinates can be used to block diagonalize automatically the secular equation occurring in the harmonic approximation of dynamics of large molecules. Examples of the usefulness of the method are given.     

Fast construction of assembly trees for molecular graphs

A number of modeling and simulation algorithms using internal coordinates rely on hierarchical representations of molecular systems. Given the potentially complex topologies of molecular systems, though, automatically generating such hierarchical decompositions may be difficult. In this article, we present a fast general algorithm for the complete construction of a hierarchical representation of a molecular system. This two-step algorithm treats the input molecular system as a graph in which vertices represent atoms or pseudo-atoms, and edges represent covalent bonds. The first step contracts all cycles in the input graph. The second step builds an assembly tree from the reduced graph. We analyze the complexity of this algorithm and show that the first step is linear in the number of edges in the input graph, whereas the second one is linear in the number of edges in the graph without cycles, but dependent on the branching factor of the molecular graph. We demonstrate the performance of our algorithm on a set of specifically tailored difficult cases as well as on a large subset of molecular graphs extracted from the protein data bank. In particular, we experimentally show that both steps behave linearly in the number of edges in the input graph (the branching factor is fixed for the second step). Finally, we demonstrate an application of our hierarchy construction algorithm to adaptive torsion-angle molecular mechanics.     

A model for the binding of low molecular weight inhibitors to the active site of thrombin

This paper describes the construction, validation and application of an active site model of the serine protease thrombin. Initial use was made of medium resolution X-ray crystallographic structures of thrombin complexed with low molecular weight, non-specific inhibitors to create a computationally useable active site shell of the enzyme. Molecular mechanics methods were then applied to dock known ligands into the active site region in order to derive a model that would accurately predict binding conformations. Validation of the modelling process was achieved by comparison of the predicted enzyme-bound conformations with their known, crystallographic binding conformations. The resultant model was used extensively for predictive purposes prior to obtaining confirmatory crystal data relating to a ligand possessing a novel and unexpected binding component complexed to thrombin. The data served both to confirm the accuracy of the binding site model and to provide information for the further refinement of the model.     

Algorithm combination strategy to obtain the second‐order advantage: simultaneous determination of target analytes in plasma using three‐dimensional fluorescence spectroscopy

Although a number of algorithms have established to obtain the well‐known second‐order advantage that quantifies analytes of interest in the presence of interferents, each has associated problems. In this work, for the first time, the optimization procedure of trilinear decomposition has been divided into three subparts, and a novel strategy is developed for assembling the advantages of the alternating trilinear decomposition (ATLD) algorithm, the self‐weighted alternating trilinear decomposition (SWATLD) algorithm, and the parallel factor analysis (PARAFAC) algorithm. The performance of the proposed strategy was evaluated using a simulated data set, a published fluorescence data set together with a new fluorescence data set that simultaneously quantifies procaine and tetracaine in plasma. Results show that the novel method can accurately and effectively estimate the qualitative and quantitative information of analytes of interest. Besides, the resolved profiles are very stable with respect to the number of components as long as the employed number is chosen to be equal or larger than the underlying one. Additionally, the study confirms that better prediction can be obtained by the new strategy when compared with ATLD, SWATLD, and PARAFAC as well as the strategy that employs direct trilinear decomposition method as initial values for PARAFAC. Moreover, the strategy can be directly extended to third‐order or higher‐order data analysis. Copyright © 2012 John Wiley & Sons, Ltd.     

Substitution effects on the molecular structures and the longitudinal molecular polarizabilities of all‐trans polyacetylene oligomers of increasing size

AM1 calculations have been performed on all‐trans polyacetylene (PA) oligomers with an increasing number of unit cells to study the effect of donor or acceptor groups capped at opposite ends of PA chains, substituents included in the monomers, substituents' number and position in the monomers, on the molecular structures, and the static longitudinal polarizabilities (α_L) and second‐order hyperpolarizabilities (γ_L). Substitution of CH₃, Cl, or F group at opposite ends of an oligomer results in an increase of α_L and γ_L, but the substitution effects on Δα_L(N) and Δγ_L(N) are very small. The asymptotic limit values are unaffected by the substitution. F substituent included in the monomer of an oligomer enhances the Δα_L(N) and Δγ_L(N) values, especially at large N, but including monomers with CH₃ or Cl substituents substantially reduces the Δα_L(N) and Δγ_L(N) values. We alter the number of F substituents included in the monomers of oligomers and find that including two F substituents in the monomer leads to the larger enhancement of Δγ_L(N). The effect of F substituents' position in the monomers of oligomers on Δα_L and Δγ_L is obvious. The results may be helpful for the design of new materials for applications in nonlinear optics, particularly in the area of poled polymer films. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Comparative analyses of a family of potential self-replicators: the subtle interplay between molecular structure and the efficacy of self-replication

It is envisioned that protocols based on self-replication will emerge as a formidable synthetic apparatus for the production of nanoscale assemblies through molecular structures that are capable of automultiplication with high reaction rates and selectivities. To achieve this goal, a complete understanding of the relationship between molecular structure and replication efficiency is necessary. Rigorous experimental and theoretical analyses of a series of self-complementary scaffolds that are intimately related in a constitutional sense, manufactured through the Diels-Alder reaction of complementary subunits, were undertaken. Experimental and computational methods were employed to map the key determinants that dictate the emergence of self-replicative function, as well as the efficiency, rate and selectivity of the self-replicative processes.     

Comparison of the numerical stability of methods for anharmonic calculations of vibrational molecular energies

On model examples, we compare the performance of the vibrational self-consistent field, variational, and four perturbational schemes used for computations of vibrational energies of semi-rigid molecules, with emphasis on the numerical stability. Although the accuracy of the energies is primarily dependent on the quality of the potential energy surface, approximate approaches to the anharmonic vibrational problem often do not converge to the same results due to the approximations involved. For furan, the sensitivity to variations of the anharmonic potential was systematically investigated by adding random noise to the cubic and quartic constants. The self-consistent field methods proved to be the most resistant to the potential variations. The second order perturbational techniques are sensitive to random degeneracies and provided the least stable results. However, their stability could be significantly improved by a simple generalization of the perturbational formula. The variational configuration interaction is practically limited by the size of the matrix that can be diagonalized for larger molecules; however, relatively fewer states need to be involved than for smaller ones, in favor of the computing.     

Alternative CHCA-based matrices for the analysis of low molecular weight compounds by UV-MALDI-tandem mass spectrometry

Analysis of low molecular weight compounds (LMWC) in complex matrices by vacuum matrix-assisted laser desorption/ionization (MALDI) often suffers from matrix interferences, which can severely degrade limits of quantitation. It is, therefore, useful to have available a range of suitable matrices, which exhibit complementary regions of interference. Two newly synthesized α-cyanocinnamic acid derivatives are reported here; (E)-2-cyano-3-(naphthalen-2-yl)acrylic acid (NpCCA) and (2E)-3-(anthracen-9-yl)-2-cyanoprop-2enoic acid (AnCCA). Along with the commonly used α-cyano-4-hydroxycinnamic acid (CHCA), and the recently developed 4-chloro-α-cyanocinnamic acid (Cl-CCA) matrices, these constitute a chemically similar series of matrices covering a range of molecular weights, and with correspondingly differing ranges of spectral interference. Their performance was compared by measuring the signal-to-noise ratios (S/N) of 47 analytes, mostly pharmaceuticals, with the different matrices using the selected reaction monitoring (SRM) mode on a triple quadrupole instrument equipped with a vacuum MALDI source. AnCCA, NpCCA and Cl-CCA were found to offer better signal-to-noise ratios in SRM mode than CHCA, but Cl-CCA yielded the best results for 60% of the compounds tested. To better understand the relative performance of this matrix series, the proton affinities (PAs) were measured using the kinetic method. Their relative values were: AnCCA > CHCA > NpCCA > Cl-CCA. This ordering is consistent with the performance data. The synthesis of the new matrices is straightforward and they provide (1) tunability of matrix background interfering ions and (2) enhanced analyte response for certain classes of compounds.     

Heuristic molecular lipophilicity potential (HMLP): a 2D-QSAR study to LADH of molecular family pyrazole and derivatives

The quantum chemical and structure-based technique heuristic molecular lipophilicity potential (HMLP) is used in the liver alcohol dehydrogenase (LADH) study of molecular family pyrazole and derivatives. The molecular lipophilic index LM, molecular hydrophilic index HM, lipophilic indices lss, and hydrophilic indices hss of the substitutes (fragments), and atomic lipophilicity indices las are constructed and used in QSAR study. The HMLP indices are correlated with bioactivities of 18 pyrazole derivatives according to the 2D QSAR procedure. The multiple linear regression equation between the bioactivities of pyrazole derivatives and HMLP indices are built using partial least square (PLS) with the optimal statistical quantity (r=0.987, s=0.479, F=47.19). The inhibition mechanism of LADH of the pyrazole derivatives is explained according to the physical meaning of HMLP indices. During the HMLP calculations for the 2D QSAR, the only input parameters are the atomic van der Waals radius without the need to resort to any empirical parameters. Accordingly, HMLP can provide a rigorous theoretical approach with a crystal clear physical meaning for the 2D QSAR.     

Using hydrogen bonds to direct the assembly of crowded aromatics

This Minireview details the design, synthesis, and self-assembly of a new class of crowded aromatics that form columnar superstructures. The assembly of these subunits produces helical and polar stacks, whose assembly can be directed with electric fields. In concentrated solutions, these self-assembled helical rods exhibit superhelical arrangements that reflect circularly polarized light at visible wavelengths. Depending on the side chains employed, spin-cast films yield either polar monolayers or isolated strands of molecules that can be visualized with scanning probe microscopy. Also detailed herein are methods to link these mesogens together to produce monodisperse oligomers that fold into defined secondary conformations.     

A novel path to luminescent hybrid molecular materials: modifying the hydroxyl group of 6‐hydroxynicotinic acid by grafting to a silica network

In this paper, a novel path was put forward to modify the hydroxyl group of 6‐hydroxynicotinic acid by 3‐(triethoxysilyl)‐propyl isocyanate and prepare the corresponding organic–inorganic molecular‐based hybrid material with the two components connected by covalent bonds. The bridging unit is a derivative of 6‐hydroxynicotinic acid that is utilized to coordinate to Tb³⁺ via hydrolysis and polycondensation processes with functional triethoxysilyl groups. Ultraviolet absorption, phosphorescence spectra and luminescence spectra were applied to characterize the photophysical properties of the hybrid material obtained and the spectroscopic data show that the triplet energy of modified 6‐hydroxynicotinic acid efficiently initiates the antenna effect and matches the emissive energy level of the metal ions. As a result, the intramolecular energy transfer process is completed within these molecular‐based hybrids. Copyright © 2005 John Wiley & Sons, Ltd.     

A new soft‐core potential function for molecular dynamics applied to the prediction of protein loop conformations

We have developed a new soft‐core potential function for the conformational search of complex systems with molecular dynamics. The potential function was designed to maintain the main equilibrium properties of the original force field, which means that the soft‐core potential gives physically realistic performance also without additional restraints, different from most of the previous soft‐core potential functions. The performance of the method was demonstrated by applying it to the problem of finding native conformations for protein loops. Short loops from neocarzinostatin and parvalbumin were used as the first test cases. The use of the new soft‐core potential function was shown to improve significantly the performance of molecular dynamics in the search of the native conformation of protein loops. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 388–397, 2000     

多取代巴比妥酸系列衍生物三阶非线性光学性质的理论研究及分子设计

在 ZINDO方法基础上 ,按完全态求和 (SOS)公式编制了计算三阶非线性光学系数γijkl的程序 ,研究了多取代巴比妥酸系列衍生物分子的结构 ,光谱和三阶非线性光学系数 γ(- ω;- ω,ω,ω) ,γ(0 ;0 ,0 ,0 ) .除了通常的 D- π- A结构外 ,还研究了 D- A-D结构 .对这些 NL O生色团分子的结构与三阶 NLO性质的关系给予系统的理论研究 .考察了给体 ,桥 ,受体变化 ,D- π- A结构及 D- A- D结构对 γ的影响 ,结论是 :1 .氧代巴比妥酸受体三阶 NLO系数高于硫代巴比妥酸受体 . 2 .芳基给体取代基与烷基给体取代基相比 ,不仅热稳定性高于后者 ,而且 γ值亦高于后者 ,从而设计了一系列有实际应用价值的热稳定性好、有优良非线性光学性质的分子     

A comparison of methods to compute the potential of mean force.

Most processes occurring in a system are determined by the relative free energy between two or more states because the free energy is a measure of the probability of finding the system in a given state. When the two states of interest are connected by a pathway, usually called reaction coordinate, along which the free-energy profile is determined, this profile or potential of mean force (PMF) will also yield the relative free energy of the two states. Twelve different methods to compute a PMF are reviewed and compared, with regard to their precision, for a system consisting of a pair of methane molecules in aqueous solution. We analyze all combinations of the type of sampling (unbiased, umbrella-biased or constraint-biased), how to compute free energies (from density of states or force averaging) and the type of coordinate system (internal or Cartesian) used for the PMF degree of freedom. The method of choice is constraint-bias simulation combined with force averaging for either an internal or a Cartesian PMF degree of freedom.     

Modeling the molecular weight distribution of block copolymer formation in a reversible addition–fragmentation chain transfer mediated living radical polymerization

Block copolymers have become an integral part of the preparation of complex architectures through self‐assembly. The use of reversible addition–fragmentation chain transfer (RAFT) allows blocks ranging from functional to nonfunctional polymers to be made with predictable molecular weight distributions. This article models block formation by varying many of the kinetic parameters. The simulations provide insight into the overall polydispersities (PDIs) that will be obtained when the chain‐transfer constants in the main equilibrium steps are varied from 100 to 0.5. When the first dormant block [polymer–S? C(Z)?S] has a PDI of 1 and the second propagating radical has a low reactivity to the RAFT moiety, the overall PDI will be greater than 1 and dependent on the weight fraction of each block. When the first block has a PDI of 2 and the second propagating radical has a low reactivity to the RAFT moiety, the PDI will decrease to around 1.5 because of random coupling of two broad distributions. It is also shown how we can in principle use only one RAFT agent to obtain block copolymers with any desired molecular weight distribution. We can accomplish this by maintaining the monomer concentration at a constant level in the reactor over the course of the reaction. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 5643–5651, 2005