An ab initio study of the electrostatics of protonated amines: application to the molecular mechanics (MM3) force field

Sorensen, Jennifer B.; Lewin, Anita H.; Bowen, J. Phillip

doi:10.1016/s0166-1280(02)00691-7

Cited by 6 publications

(2 citation statements)

References 18 publications

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Section: Resultsmentioning

confidence: 99%

“…For various ammonium derivatives MP2/6-311G(d,p) and MM3 calculations have been performed [ 106 , 299 ]. For ethyldimethylamine or [ 299 ] N -methylpiperidine [ 292 ] or the dication of β-aminotropane (relative stability of conformations 3c, 3a) the MMX or MM4-08 or MM+ fail to calculate the correct global minima. MP2 (+ 0.02 kcal mol −1 , + 0.05 kcal mol −1 , + 0.07 kcal mol −1 ), B3LYP (+ 0.13 kcal mol −1 , + 0.36 kcal mol −1 , − 0.28 kcal mol −1 ), HF/cc-pVDZ (+ 0.15 kcal mol −1 , + 0.55 kcal mol −1 , + 0.03 kcal mol −1 ), HF/cc-pVTZ (+ 0.23 kcal mol −1 , + 0.65 kcal mol −1 , + 0.03 kcal mol −1 ), HF/CBS (+ 0.33 kcal mol −1 , + 0.69 kcal mol −1 , + 0.03 kcal mol −1 ) and MM3-00 (− 0.24 kcal mol −1 , − 0.50 kcal mol −1 , + 0.38 kcal mol −1 ) performed with the smaller devations following by MMFF94 (− 0.08 kcal mol −1 , − 0.15 kcal mol −1 , − 4.33 kcal mol −1 ) and MM3-00 (− 0.24 kcal mol −1 , − 0.50 kcal mol −1 , − 1.23 kcal mol −1 ).…”

Section: Resultsmentioning

confidence: 99%

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Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

Stylianakis,

Zervos,

Lii

et al. 2023

J Comput Aided Mol Des

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We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger’s force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree–Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol−1), followed by B3LYP (0.69 kcal mol−1) and the HF theories (0.81–1.0 kcal mol−1). As regards the force fields, the lowest errors were observed for the Allinger’s force fields MM3-00 (1.28 kcal mol−1), ΜΜ3-96 (1.40 kcal mol−1) and the Halgren’s MMFF94 force field (1.30 kcal mol−1) and then for the MM2-91 clones MMX (1.77 kcal mol−1) and MM+ (2.01 kcal mol−1) and MM4 (2.05 kcal mol−1). The DREIDING (3.63 kcal mol−1) and UFF (3.77 kcal mol−1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization. Graphical abstract

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

Stylianakis,

Zervos,

Lii

et al. 2023

J Comput Aided Mol Des

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Absolute Stereochemical Determination of Chiral Carboxylates Using an Achiral Molecular Tweezer

Yoon

Lee

Jang

2012

Chemistry A European J

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A new type of molecular tweezer (1) has been synthesized for the direct determination of the absolute configuration of chiral carboxylates without analyte derivatization. Upon the addition of diamine and anionic guests, 1 exhibited shifts in its absorption spectrum with clear isosbestic points. The continuous variation method indicated that both the diamine and anionic guests form 1:1 host-guest complexes with 1 with very high binding affinity. When Boc-L-Ala (BLA) as a form of tetrabutylammonium salt was added to 1, a weak negative CD signal was observed. This weak CD signal was dramatically changed to a strong positive CD couplet upon addition of achiral 1,12-diaminododecane. Such a positive CD couplet was observed for all of the tested L-amino acid derivatives, while the D-amino acid derivatives gave the opposite signals. As a result of these unique characteristics of 1, it can be utilized as a highly sensitive probe for the absolute stereochemical determination of chiral carboxylates.

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Metal–Metal Bonding in Bridging Hydride and Alkyl Compounds

Parkin

2010

Structure and Bonding

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An ab initio study of the electrostatics of protonated amines: application to the molecular mechanics (MM3) force field

Cited by 6 publications

References 18 publications

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory

Absolute Stereochemical Determination of Chiral Carboxylates Using an Achiral Molecular Tweezer

Metal–Metal Bonding in Bridging Hydride and Alkyl Compounds

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