Substituted hydrocarbon: a CCSD(T) and local vibrational mode investigation

Delgado, Alexis Antoinette Ann; Sethio, Daniel; Matthews, Devin A.; Oliveira, Vytor; Kraka, Elfi

doi:10.1080/00268976.2021.1970844

Cited by 3 publications

(2 citation statements)

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“…[ 133 ], and hydrogen bonds [ 30 , 134 , 135 , 136 , 137 , 138 , 139 , 140 , 141 , 142 ]. Recently, the quantitative assessment of bond strength in biological systems applying a QM/MM methodology [ 143 , 144 , 145 ] and the analysis of bonding in actinide and lanthanide compounds have been added to the LMA repertoire [ 146 , 147 , 148 ]. LMA also successfully revised a number of concepts, such as the characterization of metal-ligand interactions, replacing the Tolman electronic parameter (TEP) with the more accurate metal-ligand electronic parameter (MELP), based on local mode force constants [ 149 , 150 , 151 , 152 , 153 ].…”

Section: Methodsmentioning

confidence: 99%

Quantum Mechanical Assessment of Protein–Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory

Madushanka

Moura

Verma

et al. 2023

IJMS

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Hydrogen bonds (HB)s are the most abundant motifs in biological systems. They play a key role in determining protein–ligand binding affinity and selectivity. We designed two pharmaceutically beneficial HB databases, database A including ca. 12,000 protein–ligand complexes with ca. 22,000 HBs and their geometries, and database B including ca. 400 protein–ligand complexes with ca. 2200 HBs, their geometries, and bond strengths determined via our local vibrational mode analysis. We identified seven major HB patterns, which can be utilized as a de novo QSAR model to predict the binding affinity for a specific protein–ligand complex. Glycine was reported as the most abundant amino acid residue in both donor and acceptor profiles, and N–H⋯O was the most frequent HB type found in database A. HBs were preferred to be in the linear range, and linear HBs were identified as the strongest. HBs with HB angles in the range of 100–110, typically forming intramolecular five-membered ring structures, showed good hydrophobic properties and membrane permeability. Utilizing database B, we found a generalized Badger’s relationship for more than 2200 protein–ligand HBs. In addition, the strength and occurrence maps between each amino acid residue and ligand functional groups open an attractive possibility for a novel drug-design approach and for determining drug selectivity and affinity, and they can also serve as an important tool for the hit-to-lead process.

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Section: Methodsmentioning

confidence: 99%

Quantum Mechanical Assessment of Protein–Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory

Madushanka

Moura

Verma

et al. 2023

IJMS

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“…[42] The normal vibrational stretching frequencies are also used for identification purposes; however, those quantities are typically plagued by electronic and kinematic couplings, which can lead to anomalous results and disconnected property relationships. The vibrational signatures associated with the local stretching force constants, on the other hand, are decoupled from the monomer interactions and have been demonstrably shown to accurately portray the intrinsic bond strengths [43] of substituted alkynes, [44] intermolecular HBs, [45] pnicogen bonds, [46,47] chalcogen bonds, [48] and XBs. [42,49] Graphitic carbon nitride building blocks, namely melamine and heptazine, are known for their highly desirable photocatalytic properties.…”

Section: Introductionmentioning

confidence: 99%

Shedding Light on the Vibrational Signatures in Halogen‐Bonded Graphitic Carbon Nitride Building Blocks

et al. 2023

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The relative contributions of halogen and hydrogen bonding to the interaction between graphitic carbon nitride monomers and halogen bond (XB) donors containing CÀ X and C�C bonds were evaluated using computational vibrational spectroscopy. Conventional probes into select vibrational stretching frequencies can often lead to disconnected results. To elucidate this behavior, local mode analyses were performed on the XB donors and complexes identified previously at the M06-2X/ aVDZ-PP level of theory. Due to coupling between low and high energy CÀ X vibrations, the C�C stretch is deemed a better candidate when analyzing XB complex properties or detecting XB formation. The local force constants support this conclusion, as the C�C values correlate much better with the σ-hole magnitude than their CÀ X counterparts. The intermolecular local stretching force constants were also assessed, and it was found that attractive forces other than halogen bonding play a supporting role in complex formation.

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Allowable stretching bond force constants on carbon nanomaterials: A DFT study

Medina

Cab

Casais-Molina

et al. 2022

Diamond and Related Materials

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Substituted hydrocarbon: a CCSD(T) and local vibrational mode investigation

Abstract: This supplementary material includes Table S1 which features the atomic cartesian coordinates in Å for systems 1-40 obtained at the CCSD(T)/cc-pVTZ level of theory with the exception of system 33 which was calculated with CCSD(T)/cc-pVDZ.

Cited by 3 publications

References 113 publications

Quantum Mechanical Assessment of Protein–Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory

Quantum Mechanical Assessment of Protein–Ligand Hydrogen Bond Strength Patterns: Insights from Semiempirical Tight-Binding and Local Vibrational Mode Theory

Shedding Light on the Vibrational Signatures in Halogen‐Bonded Graphitic Carbon Nitride Building Blocks

Allowable stretching bond force constants on carbon nanomaterials: A DFT study

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