The fragment molecular orbital and systematic molecular fragmentation methods applied to water clusters

Two electronic structure methods, the fragment molecular orbital (FMO) and systematic molecular fragmentation (SMF) methods, that are based on fragmenting a large molecular system into smaller, more computationally tractable components (fragments), are presented and compared with fully ab initio results for the predicted binding energies of water clusters. It is demonstrated that, even when explicit three-body effects are included (especially necessary for water clusters due to their complex hydrogen-bonded networks) both methods present viable, computationally efficient alternatives to fully ab initio quantum chemistry.     

Molecular cluster building algorithm: electrostatic guidelines and molecular tailoring approach

Nano-sized clusters of various materials are recent experimental targets, since they exhibit size-dependent physico-chemical properties. A vast amount of literature is available on the study of molecular clusters but general methods for systematic evolution of their growth are rather scarce. The present work reports a molecular cluster building algorithm based on the electrostatic guidelines, followed by ab initio investigations, enabled by the application of molecular tailoring approach. Applications of the algorithm for generating geometries and interaction energies of large molecular clusters of zinc sulfide, benzene, and water are presented.     

Different approaches to conformational analysis: A comparison of completeness,efficiency, and reliability based on the study of a nine-membered lactam

Different methods such as molecular dynamics, systematic, or stochastic search and a special “generic shape” algorithm have been employed in the conformational analysis of a nine-membered lactam. Furthermore, crystal data were used to generate conformations of the compound under consideration. The various methods are compared in terms of their efficiency and completeness in the search for conformations with an energy content of up to 60 kJ/mol above the global minimum. Additionally, the generated conformations have been optimized by different techniques, molecular mechanics and quantum chemical calculations, to compare the number of existing local minima and their relative energies and geometries.     

On the Stability of Cyclophane Derivates Using a Molecular Fragmentation Method

A molecular fragmentation method is used to study the stability of cyclophane derivates by decomposing the molecular energy into the molecular strain and intramolecular interaction energies. The molecular strain energies obtained by utilising the fragmentation method are in good agreement with existing experimental data. The intramolecular interaction energies calculated as the difference between the supermolecular energy and the bonded fragment energies are repulsive in the cyclophanes studied. The nature of this interaction is studied for groups of systematically extended doubled layered paracyclophane systems using the random‐phase approximation (RPA), two recently developed extensions to the RPA and standard density functional theory (DFT) methods including dispersion corrections. Upon a systematic increase in conjugation the strongly repulsive intramolecular interaction energy reduces and thus leads to an increase in the stability. Finally, existing experimental and theoretical estimates of the molecular strain are compared with the results of this work.     

Correction of systematic errors in CORE processing of DOSY data

DOSY data for mixtures are commonly processed either by single channel methods (e.g. HR-DOSY) or multichannel methods (e.g. CORE). Both aim to separate the signals from species of different molecular sizes by their diffusion coefficients; the result is displayed either as a 2D plot (as in HR-DOSY) or as individual spectra (as in CORE). Both types of methods are sensitive to any systematic errors in the experimental data. The effects of, and remedies for, two such sources of error, spatially non-uniform pulsed field gradients (PFGs) and instrument instability, are demonstrated for CORE processing, using a corrected form of the Stejskal-Tanner equation and reference deconvolution, respectively.     

Computational chemistry applied to the design of chiral stationary phases for enantiomeric separation

A general computational scheme for the rational design of chiral stationary phases for the chromatographic separation of enantiomers has been established. The developed scheme was based on applying different interaction models (force field methods versus semi empirical quantum chemical methods), different docking algorithms (systematic grid search methods versus interactive methods guided by rules based on binding modes) and different levels of approximations (rigid versus flexible docking) to a representative test problem containing the 3,5-dinitrobenzoyl group. The computational methods in use covered the most sophisticated methods which could presently be applied to problems of such a size (about 80 atoms). It has been shown that the current computational approaches using rigid body approximations for the docked molecules and simple molecular mechanics (not taking pi-“effects” into account) are invalid in view of the required predictive precision of about 1–2 Kcal/mole for the differential binding energy. Another surprising result was the failure of the commonly used systematic search methods in determining the most favorable binding modes. Based on our calculations on the representative test problem we propose a new arrangement for the most stable complexes without parallel stacking of the aromatic pi-donor and the 3,5-dinitrobenzoyl pi-acceptor systems.     

光系统Ⅱ抑制剂—反式氰基丙烯酸酯比较分子场和电子结构研究

对反式氰基丙烯酸酯系列活性分子采用限制性系统搜索方法确定的药效团模型 ,与 9类不同骨架结构的光系统 抑制剂 DISCO模型中的反式氰基丙烯酸酯分子(M- 2 2 )的活性构象为模板所确定的药效团模型是非常相近的。对两种方法所获得的活性构象分子进行了 Co MFA研究 ,其结果是一致的。采用 PM3方法进行了量子化学计算 ,计算结果表明两种模型的构象分子具有相近的电子结构 ,根据分子静电场、立体场和电子结构探讨了该类抑制剂的构效关系。     

Molecular representation of coal-derived asphaltene based on high resolution mass spectrometry

The asphaltene separated by solubility in small molecular alkanes and toluene is the most structurally diverse and complex components in heavy oil, such as vacuum residue and coal tar. The coal-derived asphaltene is always regard as a succession of maltene fraction from small molecules to large molecules, and also a continuum of island- and archipelago-type structures, which is difficult to be identified accurately through current characterization methods. This limits the further study of molecular dynamics and reaction dynamics simulation of asphaltenes. In this work, a representation model of molecular composition and structure for coal-derived asphaltene is developed mainly based on Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) coupled with collision induced dissociation (CID) and traditional methods of nuclear magnetic resonance spectroscopy (¹³C NMR), Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS). Island- and archipelago-type structures are considered qualitatively in the representation of asphaltene. The asphaltene molecules are systematic assembled using stochastic algorithms and optimized by simulated annealing algorithm according to the group contribution method. The bulk properties for simulating asphaltenes are in good agreement with the experimental results giving acceptable predictions for the composition and structure of the asphaltenes. Moreover, the representative average structure asphaltene molecules are obtained using the developed molecular similarity function, which could be applied in the further study of molecular aggregation simulation and reaction kinetics simulation.     

Excited state geometries within time-dependent and restricted open-shell density functional theories

Singlet excited state geometries of a set of medium sized molecules with different characteristic lowest excitations are studied. Geometry optimizations of excited states are performed with two closely related restricted open-shell Kohn–Sham methods and within linear response to time-dependent density functional theory. The results are compared to wave-function based methods. Excitation energies (vertical and adiabatic) calculated from the open-shell methods show systematic errors depending on the type of excitation. However, for all states accessible by the restricted methods a good agreement for the geometries with time-dependent density functional theory and wave-function based methods is found. An analysis of the energy with respect to the mixing angle for the singly occupied orbitals reveals that some states (mostly [n→π^*]) are stable when symmetry constraints are relaxed and others (mostly [π→π^*]) are instable. This has major implications on the applicability of the restricted open-shell methods in molecular dynamics simulations.     

Self-consistent group calculations on polyatomic molecules V. Molecules with a double or triple bond

SCGF calculations are reported for the ground state of ethylene, formaldehyde, acetylene and hydrogen cyanide. A minimum basis of contracted Gaussians was used and optimum hybridization was determined for each of the molecules by systematic variation of the hybridization parameters until the total electronic energy was a minimum. Properties of CH bonds as well as CC, CO and CN σ and π bonds are discussed in some detail. The results show that the assumption of transferable framework integrals β, basic to all semiempirical methods of calculating molecular wave functions, is strictly justified within the SCGF method.     

Molecular size and conformational effects on oligophenylene's electronic and vibrational properties

Electronic and vibrational properties of phenylene‐based oligomers from biphenyl P2P to para‐sexiphenil P6P, and their dependence on torsion angle are calculated using semiempirical quantum mechanic (AM1, ZINDO/S) and ab initio linear combination of atomic orbitals methods. The systematic relations between molecular size and geometry, and numerous molecular properties have been established, providing the basis both for the spectroscopic identification of different structures that could appear during material processing and for tailoring of devices with desired properties. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1783–1794, 2006     

Symmetry groups and representations of hamiltonians for several coupled degrees of freedom: Application to non-rigid molecular vibrations

We present a systematic method of determining finite symmetry groups for multiple coordinate hamiltonians including coupling terms. Groups are first derived separately for terms involving single coordinates. When these terms are added together, direct products of the initial groups are taken, and more symmetry operations may need to be included which involve several coordinates. When coupling terms are included, some symmetry operations must be discarded and subgroups of the product group determined. The determination of the classes, the induction and subduction of irreducible representations and characters, and assignment of molecular properties to these representations are performed along with the group derivation. We discuss the application of these methods to hamiltonians for non-rigid molecular vibrations in four membered ring molecules, molecules with two methyl groups, and the pseudorotation interconversion motion of some MX₅ molecules.     

Detecting Reaction Pathways and Computing Reaction Rates in Condensed Phase

Methods for the computation of rate constants that characterize classical reactions occurring in the condensed phase are discussed. While microscopic expressions for these transport properties are well known, their computation presents challenges for simulation since reactive events often occur rarely, and the long time scales that are typical for reactive processes are not accessible using simple molecular dynamics methods. Furthermore, the underlying free energy surface is very complex with many saddle points that prevent sampling of possible reaction pathways. As a result, the reaction coordinate may be a complex many-body function of the system’s degrees of freedom. Since there is not an a priori way to define a “good” reaction coordinate, methods are being developed to assist in a systematic construction of a reaction coordinate. These methods are reviewed and examples of non-trivial reaction coordinates are presented.     

Aptamers as analytical reagents

Many important analytical methods are based on molecular recognition. Aptamers are oligonucleotides that exhibit molecular recognition; they are capable of specifically binding a target molecule, and have exhibited affinity for several classes of molecules. The use of aptamers as tools in analytical chemistry is on the rise due to the development of the "systematic evolution of ligands by exponential enrichment" (SELEX) procedure. This technique allows high-affinity aptamers to be isolated and amplified when starting from a large pool of oligonucleotide sequences. These molecules have been used in flow cytometry, biosensors, affinity probe electrophoresis, capillary electrochromatography, and affinity chromatography. In this paper, we will discuss applications of aptamers which have led to the development of aptamers as chromatographic stationary phases and applications of these stationary phases; and look towards future work which may benefit from the use of aptamers as stationary phases.     

Advance of computational technology for simulating solvent extraction.

Due to recent significant enhancement of computer performance as well as computational techniques, molecular modeling and molecular simulations using computational chemistry can be achieved at the level of practical applications. Even in solvent extraction, the application of computational chemistry to simulations of extraction processes and the molecular design of high-performance extracting agents have gradually been increasing during the last decade. With combining the quantitative structure-property relationship between the molecule properties calculated by the computational chemistry methods and the thermodynamic properties obtained from experiments, researchers can precisely predict the next-generation of extracting agents and novel extraction processes. In this review, the concept of computational chemistry, such as molecular mechanics, molecular orbitals and molecular dynamics calculations, frequently used in the filed of solvent extraction, are outlined. Our systematic research on the solvent-extraction process utilizing MM, MO and MD calculations is also presented.     

Simulations of internal rotation potential energies for substituted ethanes

Two approaches to the simulation of internal rotation potential energies in substituted ethanes are formulated for general applications. Called the vicinal Fourier coefficient and vicinal pair energy methods, they differ only in form. The latter procedure has the advantage of yielding energy terms that represent pairwise interactions between vicinal substitutents. As numerical examples, the potential energies of ethane and five of its simple methyl and chloro derivatives are employed to simulate the corresponding energies of two higher derivatives of the series. The initial energy data were calculated by the molecular mechanics method (MM2) with geometry optimizations and the ab initio MO procedure (STO-3G) with standard geometries. Results indicate that simulated energies are reasonably accurate for the flexible-rotor model (MM2) and extremely accurate for the rigid-rotor model (STO-3G). Deviations appear to be systematic and may be rationalized on the basis of molecular structure.     

Quantum study of peroxidic bonds and torsional levels for ROOR' molecules (R, R'=H, F, Cl, NO, CN)

We present here a systematic study by quantum mechanical methods of a series of molecules (HOOF, HOOCl, HOONO, HOOCN, FOOF, ClOOF, ClOOCl, and FOONO), corresponding to substitutions of one or both hydrogens in hydrogen peroxide. The emphasis is on the structural and energetic properties and on the features of the internal modes, in particular, the torsion around the O-O bond, which leads to the chirality changing isomerization. The cis and trans barriers appear to vary remarkably upon substitution by halogen groups. They are compared with experimental and theoretical information, when available, and analyzed by reference to a previous systematic analysis of the effects of alkyl substitutions. Torsional levels were calculated, and their distribution as a function of temperature was determined. This information is of interest for statistical approaches to equilibrium properties and to rates of processes where torsional anharmonicity is relevant, as required for recent atmospheric modeling studies and also for prototypical chiral separation experiments, in view of a possible dynamic mechanism for chirality exchange by molecular collisions. Dipole moments are also presented.     

Prediction of protein structural classes and subcellular locations

The structural class and subcellular location are the two important features of proteins that are closely related to their biological functions. With the rapid increase in new protein sequences entering into data banks, it is highly desirable to develop a fast and accurate method for predicting the attributes of these features for them. This can expedite the functionality determination of new proteins and the process of prioritizing genes and proteins identified by genomics efforts as potential molecular targets for drug design. Various prediction methods have been developed during the last two decades. This review is devoted to presenting a systematic introduction and comparison of the existing methods in respect to the prediction algorithm and classification scheme. The attention is focused on the state-of-the-art, which is featured by the covarient-discriminant algorithm developed very recently, as well as some new classification schemes for protein structural classes and subcellular locations. Particularly, addressed are also the physical chemistry foundation of the existing prediction methods, and the essence why the covariant-discriminant algorithm is so powerful.