Theory of the hydrogen bond

Kollman, Peter A.; Allen, Leland C.

doi:10.1021/cr60277a004

Cited by 718 publications

(309 citation statements)

References 28 publications

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“…All levels of calculations show that the C 7 The dimer geometries are consistent with the binding energies; the dimers with larger binding energies (i.e., Aββ-C 7 and Aββ-C 7 ′) have shorter H⋯N H-bonds than Aββ-C 5 and Aββ-C 5 ′ (see Figure 2), respectively. Compared to the helical αHH′ dimer, the methyl groups in Aββ-C 5 ′ and Aββ-C 7 ′ have limited influence on the alignment of two H-bonds, and the H-bond angles in the two antiparallel β dimers are very close (see Figure 2).…”

Section: Interaction Energies In H-bond Pairsmentioning

confidence: 53%

“…The unblocked set has the advantage to avoid the steric disturbance of the blocking methyl groups, whereas the H-bond donors and acceptors in the methyl-blocked set have the chemical-bonding environment closer to protein peptides. The four dimers in the unblocked set hereafter are referred to as αHH for the H-bond pairs in the α helix, Aββ-C 5 and Aββ-C 7 for the H-bond pairs in the antiparallel β sheet, and Pββ for the H-bond pairs in the parallel β sheet. Their counterparts in the methyl-blocked set are labeled as αHH′, Aββ-C 5 ′, Aββ-C 7 ′, and Pββ′, respectively.…”

Section: Methodsmentioning

confidence: 99%

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Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures

Wang

Lei

et al. 2007

J. Chem. Theory Comput.

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Ab initio calculations up to the MP2/aug-cc-pVQZ//MP2/6-311+G** level have been carried out to characterize the four patterns of hydrogen-bond (H-bond) pairs in protein secondary structures. The unblocked and methyl-blocked glycine dipeptide dimers were arranged to model the H-bond pairs in α-helix (αHH) and antiparallel (Aββ-C 5 and Aββ-C 7 ) and parallel β-sheet (Pββ) secondary structures. The study uncovers that, in addition to the primary CO⋯NH H-bonds and the crossing secondary interactions, the CH⋯OC H-bonds and the tertiary effect (as we call it) also contribute substantially. The tertiary effect is due to the interpolarization between the donor and acceptor of a H-bond. This effect, which enhances the dipole-dipole interactions between two nearby H-bonds, stabilizes the β-sheet-like but destabilizes the helix-like H-bond pairs. The MP2 binding energies of the complexes were further refined by extrapolating to the complete basis set limit (CBS) according to Truhlar and co-workers and by a three-basis-set-based method. The best extrapolated CBS(aD-aT-aQ) binding energies of the unblocked dimers are −13.1 (αHH), −11.3 (Aββ-C 5 ), −19.2 (Aββ-C 7 ), and −14.8 kcal/mol (Pββ). For the methyl-blocked counterparts, the best extrapolated CBS(D-T-Q) binding energies are −14.8, −13.4, −20.8, and −16.7 kcal/mol, respectively. The interactions in the parallel β conformations are very close to the averages of the C 5 and C 7 antiparallel β conformations, and both are stronger than the helical dimers. Because the additive force fields are unable to account for the tertiary effect owing to the lack of polarization, all examined additive force fields significantly overestimate the interaction energies of the helix conformations relative to the β-sheet conformations. Notably, the agreement between molecular mechanical and quantum mechanical binding energies is improved after turning on the polarization. The study provides reference ab initio structures and binding energies for characterizing the backbone H-bonds of the protein secondary structures, which can be used for the parametrization of empirical molecular mechanics force fields.

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Section: Interaction Energies In H-bond Pairsmentioning

confidence: 53%

Section: Methodsmentioning

confidence: 99%

Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures

Wang

Lei

et al. 2007

J. Chem. Theory Comput.

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“…The halides, which were obtained crystalline under their monohydrated form, crystallize in common space groups (2: P2 1 /n, 3: P2 1 /c, 4: P-1) and follow the trend of rising densities (2: 1.73 < 3: 2.02 < 4: 2.34 g cm -3 ). All three structures are dominated by many hydrogen bonds [16][17][18] involving the crystal water molecules. Figure 2 shows the molecular structure of 2.…”

Section: Single Crystal X-ray Structure Analysismentioning

confidence: 99%

Inorganic Amino-Nitro-Guanidinium Derivatives

Fischer¹,

Klapötke²,

Lux³

et al. 2012

Crystals

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1-Amino-3-nitroguanidine (ANQ, 1) was synthesized by hydrazinolysis of nitroguanidine (NQ) with hydrazine hydrate. Four different amino-nitroguanidinium salts (chloride (2), bromide (3), iodide (4) and sulfate (5)) were synthesized and structurally characterized by low-temperature X-ray diffraction. The halides 2-4 could only be obtained crystalline as monohydrates. In addition, they were characterized by NMR and vibrational spectroscopy, elemental analysis and the sensitivities towards impact, friction and electrostatic discharge were determined. The compounds can be used in silver (AgX, X = Cl, Br, I) and barium (BaSO 4 ) based metathesis reactions in order to form more complex salts of 1-amino-nitroguanidine.

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“…The H-bond is an intermediate range intermolecular interaction between electron-deficient hydrogen and a region of high electron density. Its fundamental role in the structure of DNA and the secondary and tertiary structure of proteins is well known (Kollman and Allen, 1972). In many crystal lattices of organic compounds the H-bonds are a decisive factor governing the molecular packing.…”

Section: Hydrogen Bonds and Vibrational Spectroscopy 21 Description mentioning

confidence: 99%

Structure Characterization of Materials by Association of the Raman Spectra and X-Ray Diffraction Data

Chagas¹,

Souza²,

Carmo³

et al. 2012

Vibrational Spectroscopy

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Theory of the hydrogen bond

Cited by 718 publications

References 28 publications

Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures

Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures

Inorganic Amino-Nitro-Guanidinium Derivatives

Structure Characterization of Materials by Association of the Raman Spectra and X-Ray Diffraction Data

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