Probing hydrogen bond potential surfaces for out-of-plane geometries: Near-infrared combination band torsional (ν6) spectroscopy in (HCl)2

2003 ◽  
Vol 118 (22) ◽  
pp. 10137-10148 ◽  
Author(s):  
Michal Fárnı́k ◽  
Scott Davis ◽  
David J. Nesbitt
Keyword(s):  
Hydrogen Bond ◽  
Near Infrared ◽  
Potential Surfaces ◽  
Combination Band ◽  
Out Of Plane

Infrared combination band intensities of CH out-of-plane vibrations for pyridine and its deuterium derivatives in CS2 solution

1986 ◽  
Vol 117 (1) ◽  
pp. 30-37 ◽  
Author(s):  
Tetsuro Yamamoto ◽  
Ryoji Mitsuhashi ◽  
Minoru Akiyama ◽  
Yuzo Kakiuti
Keyword(s):  
Combination Band ◽  
Out Of Plane

Plucking a hydrogen bond: A near infrared study of all four intermolecular modes in (DF)2

1996 ◽  
Vol 105 (16) ◽  
pp. 6645-6664 ◽  
Author(s):  
Scott Davis ◽  
David T. Anderson ◽  
David J. Nesbitt
Keyword(s):  
Hydrogen Bond ◽  
Near Infrared ◽  
Infrared Study

The crystal structure of Proteus vulgaris tryptophan indole-lyase complexed with oxindolyl-L-alanine: implications for the reaction mechanism

2018 ◽  
Vol 74 (8) ◽  
pp. 748-759
Author(s):  
Robert S. Phillips ◽  
Adriaan A. Buisman ◽  
Sarah Choi ◽  
Anusha Hussaini ◽  
Zachary A. Wood
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Aromatic Ring ◽  
Active Site ◽  
Enzymatic Reaction ◽  
Proteus Vulgaris ◽  
Bacterial Enzyme ◽  
Small Domain ◽  
Out Of Plane ◽  
Reversible Formation

Tryptophan indole-lyase (TIL) is a bacterial enzyme which catalyzes the reversible formation of indole and ammonium pyruvate from L-tryptophan. Oxindolyl-L-alanine (OIA) is an inhibitor of TIL, with a K i value of about 5 µM. The crystal structure of the complex of Proteus vulgaris TIL with OIA has now been determined at 2.1 Å resolution. The ligand forms a closed quinonoid complex with the pyridoxal 5′-phosphate (PLP) cofactor. The small domain rotates about 10° to close the active site, bringing His458 into position to donate a hydrogen bond to Asp133, which also accepts a hydrogen bond from the heterocyclic NH of the inhibitor. This brings Phe37 and Phe459 into van der Waals contact with the aromatic ring of OIA. Mutation of the homologous Phe464 in Escherichia coli TIL to Ala results in a 500-fold decrease in k cat/K m for L-tryptophan, with less effect on the reaction of other nonphysiological β-elimination substrates. Stopped-flow kinetic experiments of F464A TIL show that the mutation has no effect on the formation of quinonoid intermediates. An aminoacrylate intermediate is observed in the reaction of F464A TIL with S-ethyl-L-cysteine and benzimidazole. A model of the L-tryptophan quinonoid complex with PLP in the active site of P. vulgaris TIL shows that there would be a severe clash of Phe459 (∼1.5 Å apart) and Phe37 (∼2 Å apart) with the benzene ring of the substrate. It is proposed that this creates distortion of the substrate aromatic ring out of plane and moves the substrate upwards on the reaction coordinate towards the transition state, thus reducing the activation energy and accelerating the enzymatic reaction.

scholarly journals Distinct Difference in Sensitivity of NIR vs. IR Bands of Melamine to Inter-Molecular Interactions with Impact on Analytical Spectroscopy Explained by Anharmonic Quantum Mechanical Study

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1402 ◽  
Author(s):  
Justyna Grabska ◽  
Krzysztof B. Beć ◽  
Christian G. Kirchler ◽  
Yukihiro Ozaki ◽  
Christian W. Huck
Keyword(s):  
Vibrational Spectroscopy ◽  
Molecular Interactions ◽  
Near Infrared ◽  
Three Dimensions ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Spectral Simulation ◽  
Analytical Spectroscopy ◽  
Quality Control Tool ◽  
Out Of Plane

Melamine (IUPAC: 1,3,5-Triazine-2,4,6-triamine) attracts high attention in analytical vibrational spectroscopy due to its misuse as a food adulterant. Vibrational spectroscopy [infrared (IR) and Raman and near-infrared (NIR) spectroscopy] is a major quality control tool in the detection and quantification of melamine content. The physical background for the measured spectra is not interpreted in analytical spectroscopy using chemometrics. In contrast, quantum mechanical calculations are capable of providing deep and independent insights therein. So far, the NIR region of crystalline melamine has not been studied by quantum mechanical calculations, while the investigations of its IR spectra have remained limited. In the present work, we employed fully anharmonic calculation of the NIR spectrum of melamine based on finite models, and also performed IR spectral simulation by using an infinite crystal model—periodic in three dimensions. This yielded detailed and unambiguous NIR band assignments and revised the previously known IR band assignments. We found that the out-of-plane fundamental transitions, which are essential in the IR region, are markedly more sensitive to out-of-plane inter-molecular interactions of melamine than NIR transitions. Proper description of the chemical surrounding of the molecule of melamine is more important than the anharmonicity of its vibrations. In contrast, the NIR bands mostly arise from in-plane vibrations, and remain surprisingly insensitive to the chemical environment. These findings explain previous observations that were reported in IR and NIR analytical studies of melamine.

Single crystal polarized spectra in the near-infrared region: a local-mode analysis of the spectra of CsMnCl3•2X2O (X = H, D)

1994 ◽  
Vol 72 (5) ◽  
pp. 1211-1217 ◽  
Author(s):  
Ian M. Walker ◽  
Paul J. McCarthy
Keyword(s):  
Hydrogen Bond ◽  
Near Infrared ◽  
Infrared Region ◽  
Chloride Ions ◽  
Mode Analysis ◽  
Local Mode ◽  
Local Modes ◽  
Near Infrared Spectra ◽  
Parameter Values ◽  
Local Mode Analysis

Polarized near-infrared spectra of single crystals of CsMnCl3•2X2O (X = H, D) were recorded at 10 K. Those bands which could be assigned to O—H or O—D stretch overtones were analyzed using local-mode theory specifically adapted for systems having less than C2v symmetry. Both O—H oscillators form nearly linear hydrogen bonds to neighboring chloride ions at different distances. As a result, the local-mode harmonic frequency and anharmonicity parameters show characteristic shifts from their gas-phase values. The parameter values cover an unusually narrow range in this crystal, considering the spread in hydrogen-bond distances. Assignment of stretch overtone bands to specific oscillators in the crystal was made by using the polarization behavior expected of local modes in the oriented gas model. Several of the overtone bands show combinations with lattice modes or low-energy hydrogen-bond modes in unusual detail.

The infrared spectra of theobromine salts

1967 ◽  
Vol 45 (23) ◽  
pp. 2899-2902 ◽  
Author(s):  
Denys Cook ◽  
Zephyr R. Regnier
Keyword(s):  
Hydrogen Bond ◽  
Nitrogen Atom ◽  
Infrared Spectra ◽  
Imidazole Ring ◽  
Free Base ◽  
Absorption Bands ◽  
Out Of Plane ◽  
Stretching Vibrations ◽  
Deformation Modes ◽  
Infrared Absorption Bands

From the infrared spectra of theobromine salts it is concluded that the salts are probably arranged in hydrogen-bonded centrosymmetric pairs involving [Formula: see text] interactions. [Formula: see text] anion− hydrogen bonds are formed by protonation of the free nitrogen atom (N9) in the imidazole ring. Infrared absorption bands arising from the former hydrogen bond constantly appear near 3 000 cm−1, whereas those from the latter shift from 2 580 to 3 300 cm−1, depending on the anion. In-plane NH and N+H deformation modes give bands near 1 485 and 1 160 cm−1, respectively. Out-of-plane NH modes have been located, but precise assignments are not possible.The assignments for some other bands which show deuteration shifts are detailed, and the carbonyl stretching vibrations which increase in frequency on protonation of the free base are identified.

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