Natural resonance theory: I. General formalism

Glendening, Eric D.; Weinhold, Frank

doi:10.1002/(sici)1096-987x(19980430)19:6<593::aid-jcc3>3.0.co;2-m

Cited by 626 publications

(131 citation statements)

References 43 publications

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“…The computational results have been interpreted with the help of the Natural Bond Orbitals (NBO) analysis [63], [64]. NBO theory expresses the first order density matrix in terms of ‘localized’ one-center (core electrons, lone pairs) and two-centers (filled/bonding or empty/antibonding) orbitals.…”

Section: Methodsmentioning

confidence: 99%

Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

2011

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By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of Cα substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed.

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Section: Methodsmentioning

confidence: 99%

Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

2011

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“…In some cases, this interaction exhibits a partial covalent nature. Nevertheless, analysis using natural resonance theory [85] indicated ionic character rather than covalent character for all of the cases.…”

Section: Resultsmentioning

confidence: 99%

Interaction between PH3 and small water clusters: Understanding the electronic and spectroscopic properties

Viana

Silva

2015

Computational and Theoretical Chemistry

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“…The supplemental material shows a spectrum and fragmentation scheme of how some of fragments we observe in DAPC could be formed. DAPC provided low fragmentation efficiencies, which could be related to the large number of canonical forms that the molecule can adopt to stabilize intermediate radicals [69–71]. Another surprising feature of DAPC and sphingomyelin is the lack of Penning ionized peak, [M+H] 2+• , which could be attributed to a combination of the ionization energy of the [M+H] + precursor ion, competition between electronic and vibrational excitation, or the relative lability of the [M+H] 2+• product ions.…”

Section: Methods and Instrumentationmentioning

confidence: 99%

Radical-induced fragmentation of phospholipid cations using metastable atom-activated dissociation mass spectrometry (MAD-MS)

Deimler

Sander²,

Jackson

2015

International Journal of Mass Spectrometry

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The fragmentation pattern of several protonated 1+ phosphatidylcholines (PCs) were studied using low energy collision induced dissociation (CID) and helium metastable atom-activated dissociation (He-MAD). He-MAD of the protonated compounds produced a dominant phosphocholine head group at m/z 184 as well as typical sn-1 and sn-2 glycerol fragments such as [M+H–Rx-1CHC=O]+ and [M+H-Rx-1CO2H]+. Within the aliphatic chain, He-MAD showed fragments consistent with high-energy collision induced dissociation (HE-CID) and products/pathways consistent with Penning ionization of the 1+ precursor ions to their respective radical dications. These Penning ionization products included both singly and doubly charged radical fragments, and the fragment ions are related to the number and position of double bonds in the acyl chains. Fragments created through HE-CID-like fragmentation followed classic charge remote fragmentation pathways including ladder-like fragmentation along the acyl chain, except for additional or missing peaks due to predictable rearrangement reactions. He-MAD therefore shows utility in being able to effectively fragment singly charged lipids into a variety of useful product ions using both radical and high-energy processes in the confines of a 3D ion trap.

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Natural resonance theory: I. General formalism

Cited by 626 publications

References 43 publications

Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

Interaction between PH3 and small water clusters: Understanding the electronic and spectroscopic properties

Radical-induced fragmentation of phospholipid cations using metastable atom-activated dissociation mass spectrometry (MAD-MS)

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