Zeolite Structure and Reactivity by Combined Quantum-Chemical−Classical Calculations

Vries, Alex H. de; Sherwood, Paul; Collins, Simon J.; Rigby, A.M.; Rigutto, Marcello; Kramer, G.J.

doi:10.1021/jp9913012

Cited by 353 publications

(313 citation statements)

References 49 publications

(83 reference statements)

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“…In the used approach, the charge was neglected in the embedding scheme in order to prevent over-polarization. An alternative method would be the distribution of q(L M ) to its remaining binding partners [10] (only for the embedding-the force field still uses the original set of charges). While a variation of charges can surely be expected to have an influence, the fact that for the investigated nucleosides the charges q(L M ) provided by AMBER-99SB are all in the region between 0.01 and 0.07, this influence is only very minor.…”

Section: Resultsmentioning

confidence: 99%

Optimizing link atom parameters for DNA QM/MM simulations

et al. 2016

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utilize popular force fields like AMBER [9], CHARMM [8], OPLS [23] or GROMOS [35] is the ability to describe effects stemming from the intra-or intermolecular shifts of electron density for any desired chemical system. Due to this, phenomena such as charge transfers, the cleavage or formation of covalent bonds and polarization effects can be studied in-depth. Additionally, the influence of different spin states, Jahn Teller distortion and even electronic excitations can be investigated without having to resort to specifically tailored force fields.One of the major challenges for that kind of investigation is a proper description of the interface between the QM and the MM region, especially if covalent bonds are reaching through the boundary between the two regions [27]. There exist a variety of approaches to describe that frontier bond, for example capping potentials [22,26], generalized hybrid orbitals [16] or localized self-consisted field [3,33,40], but the simplest, yet very accurate [2] and therefore also highly popular [27,36] method is hydrogen capping [39].A big question regarding hydrogen-capping approaches is the proper placement of the inserted atom, so that its influence on the behavior of the surrounding atoms is minimized as much as possible. In a previous work [18], this was discussed in detail for amino acids, with the recommendation to use separate parameters for each type of sidechain to considerably improve the description of the link bond. In this work, the focus lies on the QM/MM separation of DNA nucleosides, with the C-N bond between the deoxyribose and the nucleobase acting as the link bond. Abstract This work optimizes the link bond description of the quantum mechanical/molecular mechanical separation of deoxynucleosides. The nucleosides are separated at the C-N bond between the nucleobase and the deoxyribose, with the former acting as the quantum mechanically described species. By using a flexible link atom-ansatz plus a harmonic potential to correct the energy deviation from a full quantum mechanical description, the potential energy well of the bond's stretching motion is mimicked with very high accuracy.

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Section: Resultsmentioning

confidence: 99%

Optimizing link atom parameters for DNA QM/MM simulations

et al. 2016

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“…At such a short distance, the validity of using a point charge to represent the distribution of electron density is questionable. Special treatments are applied to the MM charges near the boundary so as to avoid this unphysical polarization [33,44,70,71,82,93,110,124]. We will discuss this problem in more detail later in Sect.…”

Section: Link Atom or Local Orbital?mentioning

confidence: 99%

QM/MM: what have we learned, where are we, and where do we go from here?

2006

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This paper briefly reviews the current status of the most popular methods for combined quantum mechanical/molecular mechanical (QM/MM) calculations, including their advantages and disadvantages. There is a special emphasis on very general link-atom methods and various ways to treat the charge near the boundary. Mechanical and electric embedding are contrasted. We consider methods applicable to gas-phase organic chemistry, liquid-phase organic and organometallic chemistry, biochemistry, and solid-state chemistry. Then we review some recent tests of QM/MM methods and summarize what we learn about QM/MM from these studies. We also discuss some available software. Finally, we present a few comments about future directions of research in this exciting area, where we focus on more intimate blends of QM with MM.

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“…[33][34][35] No electrostatic cut-offs were employed in the QM/MM calculations. Electrostatic embedding [36] with the charge-shift scheme [29,37] was used to couple the QM and MM regions. Full details of the computational methodology employed in this study are available in the Supporting Information.…”

Section: Introductionmentioning

confidence: 99%

Latrunculin Analogues with Improved Biological Profiles by “Diverted Total Synthesis”: Preparation, Evaluation, and Computational Analysis

Fürstner

Kirk

Fenster

et al. 2006

Chemistry A European J

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Deliberate digression from the blueprint of the total syntheses of latrunculin A (1) and latrunculin B (2) reported in the accompanying paper allowed for the preparation of a focused library of “latrunculin‐like” compounds, in which all characteristic structural elements of these macrolides were subject to pertinent molecular editing. Although all previously reported derivatives of 1 and 2 were essentially devoid of any actin‐binding capacity, the synthetic compounds presented herein remain fully functional. One of the designer molecules with a relaxed macrocyclic backbone, that is compound 44, even surpasses latrunculin B in its effect on actin while being much easier to prepare. This favorable result highlights the power of “diverted total synthesis” as compared to the much more widely practiced chemical modification of a given lead compound by conventional functional group interconversion. A computational study was carried out to rationalize the observed effects. The analysis of the structure of the binding site occupied by the individual ligands on the G‐actin host shows that latrunculin A and 44 both have similar hydrogen‐bond network strengths and present similar ligand distortion. In contrast, the H‐bond network is weaker for latrunculin B and the distortion of the ligand from its optimum geometry is larger. From this, one may expect that the binding ability follows the order 1 ≥ 44 > 2, which is in accord with the experimental data. Furthermore, the biological results provide detailed insights into structure/activity relationships characteristic for the latrunculin family. Thus, it is demonstrated that the highly conserved thiazolidinone ring of the natural products can be replaced by an oxazolidinone moiety, and that inversion of the configuration at C16 (latrunculin B numbering) is also well accommodated. From a purely chemical perspective, this study attests to the maturity of ring‐closing alkyne metathesis (RCAM) catalyzed by a molybdenum alkylidyne complex generated in situ, which constitutes a valuable tool for advanced organic synthesis and natural product chemistry.

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Zeolite Structure and Reactivity by Combined Quantum-Chemical−Classical Calculations

Cited by 353 publications

References 49 publications

Optimizing link atom parameters for DNA QM/MM simulations

Optimizing link atom parameters for DNA QM/MM simulations

QM/MM: what have we learned, where are we, and where do we go from here?

Latrunculin Analogues with Improved Biological Profiles by “Diverted Total Synthesis”: Preparation, Evaluation, and Computational Analysis

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