Importance of selecting proper basis set in quantum mechanical studies of potential energy surfaces of carbohydrates

An extensive quantum mechanical study of a water dimer suggests that the introduction of a diffuse function into the basis set, which significantly reduces the basis set superposition error (BSSE) in the hydrogen bonding energy calculation, is the key to better calculations of the potential energy surfaces of carbohydrates. This article examines the potential energy surfaces of selected d -aldo- and d -ketohexoses (a total of 82 conformers) by quantum mechanics (QM) and molecular mechanics (MM) methods. In contrast to the results with a smaller basis set (B3LYP/6-31G** 5d), we found at the higher level calculation (B3LYP/6-311++G(2d,2p)//B3LYP/6-31G** 5d) that, in most cases, the furanose forms are less stable than the pyranose forms. These discrepancies are mainly due to the fact that intramolecular hydrogen bonding energies are overestimated in the lower level calculations. The higher level QM calculations of the potential energy surfaces of d -aldo- and d -ketohexoses now are more comparable to the MM3 results. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1593–1603, 1999     

量子化学模型方法在机械力化学中的应用

机械力化学作为一种无需溶剂的绿色化学技术得到广泛关注。然而,机械力化学反应机制需要从原子和分子尺度上深入理解力诱导的化学反应。在过去的20年中,量子化学模型方法在机械力化学机理研究中得到广泛应用,高精度量化计算可得到外力下变形分子的几何结构、能量、过渡态等诸多性质。本文介绍了目前机械力化学领域的主流量子化学模型的基本原理,同时也关注了这些模型方法在软件上的具体实现,并借助典型的案例阐述了量子化学模型在解释机械力化学机理中的作用与价值。     

Diethylamine-based ionic liquids: quantum chemical calculations and experiment

Russian Chemical Bulletin - The structural and energetic characteristics of the compounds formed by the reaction of diethylamine (DEA) with protic acids (sulfuric (H2SO4), methanesulfonic (MsOH),...     

Transition structure modeling by intersecting potential energy surfaces

A previously proposed method of modeling force field transition structures as the lowest energy structure on the seam of two intersecting potential energy surfaces is improved with respect to the force field expression and the efficiency of the optimization algorithm. Comparison with ab initio and experimental results show that the force field method may have the potential of achieving almost quantitative results. It appears that the results from transition state modeling are currently limited by the accuracy of the underlying force field. © 1994 by John Wiley & Sons, Inc.     

Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins

Contact surface area and chemical properties of atoms are used to concurrently predict conformations of multiple amino acid side chains on a fixed protein backbone. The combination of surface complementarity and solvent-accessible surface accounts for van der Waals forces and solvation free energy. The scoring function is particularly suitable for modeling partially buried side chains. Both iterative and stochastic searching approaches are used. Our programs (Sccomp-I and Sccomp-S), with relatively fast execution times, correctly predict chi1 angles for 92-93% of buried residues and 82-84% for all residues, with an RMSD of approximately 1.7 A for side chain heavy atoms. We find that the differential between the atomic solvation parameters and the contact surface parameters (including those between noncomplementary atoms) is positive; i.e., most protein atoms prefer surface contact with other protein atoms rather than with the solvent. This might correspond to the driving force for maximizing packing of the protein. The influence of the crystal packing, completeness of rotamer library and precise positioning of Cbeta atoms on the accuracy of side-chain prediction are examined. The Sccomp-S and Sccomp-I programs can be accessed through the Web (http://sgedg.weizmann.ac.il/sccomp.html) and are available for several platforms.     

Some reflections on characterizing potential surfaces for gas-phase ionic reactions

Gas phase ionic chemistry has become an essential element in our general understanding of chemical reactivity. Obtaining experimental data and then extracting information about the potential surfaces for ionic reactions in the gas phase has been critical in making the connections between gas phase and solution ionic chemistry. In this paper we discuss insights that have been important in developing some of the methodologies that are currently used in analyzing gas phase data.     

Importance of structural and chemical heterogeneity of activated carbon surfaces for adsorption of dibenzothiophene

The performance of various activated carbons obtained from different carbon precursors (i.e., plastic waste, coal, and wood) as adsorbents for the desulfurization of liquid hydrocarbon fuels was evaluated. To increase surface heterogeneity, the carbon surface was modified by oxidation with ammonium persulfate. The results showed the importance of activated carbon pore sizes and surface chemistry for the adsorption of dibenzothiophene (DBT) from liquid phase. Adsorption of DBT on activated carbons is governed by two types of contributions: physical and chemical interactions. The former include dispersive interactions in the microporous network of the carbons. While the volume of micropores governs the amount physisorbed, mesopores control the kinetics of the process. On the other hand, introduction of surface functional groups enhances the performance of the activated carbons as a result of specific interactions between the acidic centers of the carbon and the basic structure of DBT molecule as well as sulfur-sulfur interactions.     

Hydrocarbon adsorption on gold clusters: Experiment and quantum chemical modeling

Heats of adsorption Q of n-alkanes C₆–C₉ on ZrO₂ modified with gold and nickel nanoparticles were determined experimentally. The Q values were found to be higher on average by 7 kJ/mol on the modified samples as compared to the pure support. Density functional theory with the PBE functional and the pseudopotential for gold effectively allowing for relativistic corrections was used to model the adsorption of saturated hydrocarbons on Au and Au + Ni, as exemplified by the interaction of alkanes C₁–C₃ with Au _m , Au _{m − 1}Ni (m = 3, 4, 5) clusters as well as the interaction of C₁–C₈ with Au₂₀. Based on the calculation results, the probable coordination centers of alkanes on nanoparticle surfaces were found to be vertices and edges, whereas face localization was less probable.     

Adsorption of organic substances on broken clay surfaces: a quantum chemical study

Hydrogen-bonded interactions between local defect structures on broken clay surfaces modeled as molecular clusters and the organic molecules acetic acid, acetate, and N-methylacetamide (NMA) have been investigated. Density functional theory and polarized basis sets have been used for the computation of optimized interaction complexes and formation energies. The activity of the defect structures has been characterized as physical or chemical in terms of the strength of the hydrogen bonds formed. Chemical defects lead to significantly enhanced interactions with stronger hydrogen bonds and larger elongation of OH bonds in comparison to the physical defects. The type of interaction with the defect structure significantly influences the planarity of the model peptide bond in NMA. Both cases, enhancement of the planarity by increase of the CN double bond character and strong deviations from planarity, are observed.     

Dissolution of ionic crystal surfaces

The status of surface dissolution mechanisms for ionic crystals is surveyed. The mechanisms which best rationalize the unusual form of the experimental rate law for the surface dissolution of ionic crystals are described and compared. These mechanisms are effectively limited to the case of stoichiometric crystals dissolving in water. The electrochemistry of the crystal/solution interphase has not yet been satisfactorily introduced into crystal dissolution models and this extension needs more active and wider investigation.     

Non-Hermitian quantum mechanics: wave packet propagation on autoionizing potential energy surfaces

The correspondence between the time-dependent and time-independent molecular dynamic formalisms is shown for autoionizing processes. We demonstrate that the definition of the inner product in non-Hermitian quantum mechanics plays a key role in the proof. When the final state of the process is dissociative, it is technically favorable to introduce a complex absorbing potential into the calculations. The conditions which this potential should fulfill are briefly discussed. An illustrative numerical example is presented involving three potential energy surfaces.     

离子液体中硝基苯的扩散系数与量子化学参数的相关研究

采用量子化学半经验AM1方法,分别对[CMIM]+(1,3-二甲基咪唑离子)、[C2MIM]+(1-甲基-3-乙基咪唑离子)、[C4MIM]+(1-甲基-3-丁基咪唑离子)、[C6MIM]+(1-甲基-3-己基咪唑离子)和硝基苯,以及它们1∶1复合物构象进行优化,在此基础上以DFT(B3LYP/6-31+G)计算它们的...     

Differential diffusion quantum Monte Carlo method: determination of potential energy surfaces of molecules

A differential approach for self-optimizing diffusion Monte Carlo calculation was proposed in this paper, which is a new algorithm combining three techniques such as optimizing, diffusion and correlation sampling. This method can be used to directly compute the energy differential between two systems in the diffusion process, making the statistical error of calculation be reduced to order of 10-5 hartree, and recover about more than 80% of the correlation energy. We employed this approach to set up a potential energy surface of a molecule, used a "rigid move" model, and utilized Jacobi transformation to make energy calculation for two configurations of a molecule having good positive correlation. So, an accurate energy differential could be obtained, and the potential energy surface with good quality can be depicted. In calculation, a technique called "post-equilibrium remaining sample was set up firstly, which can save about 50% of computation expense. This novel algorithm was used to study the potenti