Hydrogen bond spectroscopy in the near infrared: Out‐of‐plane torsion and antigeared bend combination bands in (HF)2

1996 ◽  
Vol 105 (11) ◽  
pp. 4488-4503 ◽  
Author(s):  
David T. Anderson ◽  
Scott Davis ◽  
David J. Nesbitt
Keyword(s):  
Hydrogen Bond ◽  
Near Infrared ◽  
Out Of Plane ◽  
Combination Bands

Hydrogen-bond studies of the near infrared combination bands of the butylamines

1974 ◽  
Vol 46 (1) ◽  
pp. 89-93 ◽  
Author(s):  
J. E. Sinsheimer ◽  
Anne M. Keuhnelian
Keyword(s):  
Hydrogen Bond ◽  
Near Infrared ◽  
Combination Bands

Near-Infrared Combination and Overtone Bands of CH in CHX3, CHX2—CHX2, and CHX2—CX2—CHX2

2005 ◽  
Vol 59 (11) ◽  
pp. 1393-1398 ◽  
Author(s):  
Reikichi Iwamoto ◽  
Akishi Nara ◽  
Toshihiko Matsuda
Keyword(s):  
Excited State ◽  
Near Infrared ◽  
Present Report ◽  
Spectral Characteristics ◽  
The Other ◽  
Coupled Modes ◽  
Third Order ◽  
The Third ◽  
Combination Bands ◽  
Deformation Modes

In the present report we studied spectral characteristics of the near-infrared combination and overtone bands of CH vibrations of a CH sequence. The near-infrared bands of the CH in CHX3 (X, halogen), which were interpreted in terms of the CH stretching and CH deformation fundamentals without any ambiguity, typically showed how the frequency and intensity of a combination or an overtone depend on the vibrational excited state. In the CH–C–CH of CHX2CX2CHX2, the vibrations of one CH are isolated from those of the other CH, and the combination and overtone bands were similarly interpreted as those of the CH, although each of the combination bands was split into two because of non-degeneracy of the CH deformation. In the CH–CH of CHX2CHX2, the CH deformations only have coupled modes. The first combination showed four narrowly separate bands, which were reasonably interpreted on the basis of the CH stretching and the coupled CH deformation modes. We demonstrated that the first combination of coupled modes as well as the combination of up to, at least, the third order of isolated modes have the nature of the characteristic bands.

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

scholarly journals Anharmonicity and Spectra–Structure Correlations in MIR and NIR Spectra of Crystalline Menadione (Vitamin K3)

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6779
Author(s):  
Krzysztof B. Beć ◽  
Justyna Grabska ◽  
Christian W. Huck ◽  
Sylwester Mazurek ◽  
Mirosław A. Czarnecki
Keyword(s):  
Single Molecule ◽  
Near Infrared ◽  
Structural Information ◽  
Molecular System ◽  
Theoretical Calculations ◽  
Vitamin K3 ◽  
Structure Correlations ◽  
Mir Spectra ◽  
Combination Bands ◽  
The Relationship

Mid-infrared (MIR) and near-infrared (NIR) spectra of crystalline menadione (vitamin K3) were measured and analyzed with aid of quantum chemical calculations. The calculations were carried out using the harmonic approach for the periodic model of crystal lattice and the anharmonic DVPT2 calculations applied for the single molecule model. The theoretical spectra accurately reconstructed the experimental ones permitting for reliable assignment of the MIR and NIR bands. For the first time, a detailed analysis of the NIR spectrum of a molecular system based on a naphthoquinone moiety was performed to elucidate the relationship between the chemical structure of menadione and the origin of the overtones and combination bands. In addition, the importance of these bands during interpretation of the MIR spectrum was demonstrated. The overtones and combination bands contribute to 46.4% of the total intensity of menadione in the range of 3600–2600 cm−1. Evidently, these bands play a key role in shaping of the C-H stretching region of MIR spectrum. We have shown also that the spectral regions without fundamentals may provide valuable structural information. For example, the theoretical calculations reliably reconstructed numerous overtones and combination bands in the 4000–3600 and 2800–1800 cm−1 ranges. These results, provide a comprehensive origin of the fundamentals, overtones and combination bands in the NIR and MIR spectra of menadione, and the relationship of these spectral features with the molecular structure.

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.

Near-Infrared Spectrophotometry: A New Dimension in Clinical Chemistry

1992 ◽  
Vol 38 (9) ◽  
pp. 1623-1631 ◽  
Author(s):  
J W Hall ◽  
A Pollard
Keyword(s):  
Near Infrared ◽  
Serum Proteins ◽  
Clinical Laboratory ◽  
Clinical Chemistry ◽  
Electronic Transitions ◽  
Chemical Information ◽  
Pharmaceutical Chemical ◽  
Laboratory Measurements ◽  
Nondestructive Technique ◽  
Combination Bands

Abstract The near-infrared (NIR) spectral region (700-2500 nm) is a fertile source of chemical information in the form of overtone and combination bands of the fundamental infrared absorptions and low-energy electronic transitions. This region was initially perceived as being too complex for interpretation and consequently was poorly utilized. Advances in chemometric techniques that can extract massive amounts of chemical information from the highly overlapped, complex spectra have led to extensive use of NIR spectrophotometry (NIRS) in the food, agriculture, pharmaceutical, chemical, and polymer industries. The application of NIRS in clinical laboratory measurements is still in its infancy. NIRS is a simple, quick, nondestructive technique capable of providing clinically relevant analyses of biological samples with precision and accuracy comparable with the method used to derive the NIRS models. Analyses can be performed with little or no sample preparation and no reagents. The success of NIRS in any particular case is determined by the complexity of the sample matrix, relative NIR absorptivities of the constituents, and the wavelengths and regression technique chosen. We describe the general approach to data acquisition, calibration, and analysis, using serum proteins, triglycerides, and glucose as examples.

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.

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