Molecular Dynamics and NMR Parameter Calculations

Bernhardt, Debra Joy; Huber, Hanspeter

doi:10.1002/3527601678.ch11

Cited by 14 publications

(3 citation statements)

References 56 publications

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“…Due to the importance of solvent effects for the present problem, the question arises whether the used theoretical approach correctly mirrors the physical situation . The adaptation of the environment to changes in the electronic structure of the solute can be divided into polarization effects of the electron shells of the solvent molecules and effects resulting from molecular reorientation (rotation, translation, etc.).…”

Section: Discussionmentioning

confidence: 99%

Geometry and Cooperativity Effects in Adenosine−Carboxylic Acid Complexes

et al. 2005

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NMR experiments and theoretical investigations were performed on hydrogen bonded complexes of specifically 1- and 7-15N-labeled adenine nucleosides with carboxylic acids. By employing a freonic solvent of CDClF2 and CDF3, NMR spectra were acquired at temperatures as low as 123 K, where the regime of slow hydrogen bond exchange is reached and several higher-order complexes were found to coexist in solution. Unlike acetic acid, chloroacetic acid forms Watson-Crick complexes with the proton largely displaced from oxygen to the nitrogen acceptor in an ion pairing structure. Calculated geometries and chemical shifts of the proton in the hydrogen bridge favorably agree with experimentally determined values if vibrational averaging and solvent effects are taken into account. The results indicate that binding a second acidic ligand at the adenine Hoogsteen site in a ternary complex weakens the hydrogen bond to the Watson-Crick bound carboxylic acid. However, substituting a second adenine nucleobase for a carboxylic acid in the trimolecular complex leads to cooperative binding at Watson-Crick and Hoogsteen faces of adenosine.

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Section: Discussionmentioning

confidence: 99%

Geometry and Cooperativity Effects in Adenosine−Carboxylic Acid Complexes

et al. 2005

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“…Although this kind of approach has quite a long tradition, [15,16,18,20] there are a number of specific issues that require further consideration. Our specific strategy consists of a three-step procedure:…”

Section: Introductionmentioning

confidence: 99%

Spectroscopic Properties in the Liquid Phase: Combining High‐Level Ab Initio Calculations and Classical Molecular Dynamics

et al. 2006

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We present an integrated computational tool, rooted in density functional theory, the polarizable continuum model, and classical molecular dynamics employing spherical boundary conditions, to study the spectroscopic observables of molecules in solution. As a test case, a modified OPLS-AA force field has been developed and used to compute the UV and NMR spectra of acetone in aqueous solution. The results show that provided the classical force fields are carefully reparameterized and validated, the proposed approach is robust and effective, and can also be used by nonspecialists to provide a general and powerful complement to experimental techniques.

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“…Calculation of NMR parameters in transition-metal complexes requires both an accurate representation of the system (e.g., geometry) and environment (solution) and a high-level electronic-structure method for the NMR calculation itself. ,, Recent theoretical and implementational advances have made it possible to carry out all-electron quantum-chemical NMR calculations using a quasi-relativistic (two-component) or a fully relativistic (four-component) model with Hamiltonians including both scalar relativistic (SR) and SO interactions. , Likewise, ab initio molecular dynamics (AIMD) appears to be a particularly useful simulation technique to investigate the conformational flexibility of a system, including solvation effects and dynamical averaging of the calculated NMR chemical shifts. − Such first-principles calculations inherently account for anharmonicities, and the temperature can be set to study systems under more realistic conditions than static quantum-mechanical calculations at 0 K …”

Section: Introductionmentioning

confidence: 99%

First-Principles Calculation of ¹H NMR Chemical Shifts of Complex Metal Polyhydrides: The Essential Inclusion of Relativity and Dynamics

et al. 2020

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1 H NMR spectroscopy has become an important technique for the characterization of transition-metal hydride complexes, whose metalbound hydrides are often difficult to locate by X-ray diffraction. In this regard, the accurate prediction of 1 H NMR chemical shifts provides a useful, but challenging, strategy to help in the interpretation of the experimental spectra. In this work, we establish a density-functional-theory protocol that includes relativistic, solvent, and dynamic effects at a high level of theory, allowing us to report an accurate and reliable interpretation of 1 H NMR hydride chemical shifts of iridium polyhydride complexes. In particular, we have studied in detail the hydride chemical shifts of the [Ir 6 (IMe) 8 (CO) 2 H 14 ] 2+ complex in order to validate previous assignments. The computed 1 H NMR chemical shifts are strongly dependent on the relativistic treatment, the choice of the DFT exchange−correlation functional, and the conformational dynamics. By combining a fully relativistic four-component electronic-structure treatment with ab initio molecular dynamics, we were able to reliably model both the terminal and bridging hydride chemical shifts and to show that two NMR hydride signals were inversely assigned in the experiment.

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Molecular Dynamics and NMR Parameter Calculations

Cited by 14 publications

References 56 publications

Geometry and Cooperativity Effects in Adenosine−Carboxylic Acid Complexes

Geometry and Cooperativity Effects in Adenosine−Carboxylic Acid Complexes

Spectroscopic Properties in the Liquid Phase: Combining High‐Level Ab Initio Calculations and Classical Molecular Dynamics

First-Principles Calculation of ¹H NMR Chemical Shifts of Complex Metal Polyhydrides: The Essential Inclusion of Relativity and Dynamics

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Molecular Dynamics and NMR Parameter Calculations

Cited by 14 publications

References 56 publications

Geometry and Cooperativity Effects in Adenosine−Carboxylic Acid Complexes

Geometry and Cooperativity Effects in Adenosine−Carboxylic Acid Complexes

Spectroscopic Properties in the Liquid Phase: Combining High‐Level Ab Initio Calculations and Classical Molecular Dynamics

First-Principles Calculation of 1H NMR Chemical Shifts of Complex Metal Polyhydrides: The Essential Inclusion of Relativity and Dynamics

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Product

Resources

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First-Principles Calculation of ¹H NMR Chemical Shifts of Complex Metal Polyhydrides: The Essential Inclusion of Relativity and Dynamics