Intensities of IR bands of CH stretching vibrations and atomic charges in saturated three-membered rings

1989 ◽  
Vol 25 (12) ◽  
pp. 1342-1348
Author(s):  
I. F. Tupitsyn ◽  
Yu. V. Puzanov ◽  
A. Yu. Shibaev ◽  
A. A. Kane ◽  
S. A. Egorov
Keyword(s):  
Atomic Charges ◽  
Stretching Vibrations ◽  
Ir Bands

Vibrational study and spectra-structure correlations in magnesium disaccharinate heptahydrate, Mg(sac)2⋅7H2O

2008 ◽  
Vol 27 (1) ◽  
pp. 1
Author(s):  
Gligor Jovanovski ◽  
Petre Makreski ◽  
Bojan Šoptrajanov
Keyword(s):  
Experimental Data ◽  
Raman Spectrum ◽  
The Other ◽  
Water Molecules ◽  
Carbonyl Groups ◽  
Structural Units ◽  
Vibrational Study ◽  
Structure Correlations ◽  
Stretching Vibrations ◽  
Ir Bands

Infrared and Raman vibrational spectra of magnesium disaccharinate heptahydrate, Mg(sac)2⋅7H2O, in the 4000–380 cm–1 region (for infrared) and 4000–100 cm–1 region (for Raman) were studied. The assignment of the spectra was based on the experimental data for the previously studied metal saccharinates as well as the literature data for the ab initio calculations on the free deprotonated saccharinato species. Special attention was paid to the analysis of the H2O, CO and SO2 stretching modes. The spectral picture in the regions of the water, carbonyl and sulfonyl stretches is correlated with the number of the crystallographically determined non-equivalent H2O, CO and SO2 structural units. It was found that the presence of seven crystallographically different water molecules in the structure (fourteen different Ow⋅⋅⋅O and Ow⋅⋅⋅N distances) is not reflected in the appearance of the expected fourteen IR bands in the region of the OD stretching vibrations of the isotopically isolated HDO molecules. This must be due to the existence in the structure of several Ow⋅⋅⋅O or Ow⋅⋅⋅N hydrogen bonds with very similar strengths causing an overlap of the corresponding bands in the spectrum. Despite the presence of two carbonyl groups with practically identical C–O distances [124.2(3) and 124.0(3) pm], two clearly separated bands are registered in the carbonyl stretching region of the IR (1660 and 1627 cm–1) and Raman spectrum (1648 and 1620 cm–1). On the other hand, although two nonequivalent SO2 groups are present in the structure of Mg(sac)2⋅7H2O, only one pair of bands due to SO2 stretchings [νas(SO2 and νs(SO2) modes] is registered in the IR spectrum.

Raman and infrared spectroscopic study of the vivianite-group phosphates vivianite, baricite and bobierrite

2002 ◽  
Vol 66 (6) ◽  
pp. 1063-1073 ◽  
Author(s):  
R. L. Frost ◽  
W. Martens ◽  
P. A. Williams ◽  
J. T. Kloprogge
Keyword(s):  
Molecular Structure ◽  
Hydrogen Bonding ◽  
Water Molecules ◽  
Infrared Spectroscopic Study ◽  
Tetrahedral Symmetry ◽  
Phosphate Anions ◽  
Stretching Vibrations ◽  
Bending Modes ◽  
Ir Bands ◽  
Hydrogen Bonded

Abstract The molecular structure of the three vivianite-structure, compositionally related phosphate minerals vivianite, baricite and bobierrite of formula M32+(PO4)2.8H2O where M is Fe or Mg, has been assessed using a combination of Raman and infrared (IR) spectroscopy. The Raman spectra of the hydroxyl-stretching region are complex with overlapping broad bands. Hydroxyl stretching vibrations are identified at 3460, 3281, 3104 and 3012 cm−1 for vivianite. The high wavenumber band is attributed to the presence of FeOH groups. This complexity is reflected in the water HOH-bending modes where a strong IR band centred around 1660 cm−1 is found. Such a band reflects the strong hydrogen bonding of the water molecules to the phosphate anions in adjacent layers. Spectra show three distinct OH-bending bands fromstrongly hydrogen-bonded, weakly hydrogen bonded water and non-hydrogen bonded water. The Raman phosphate PO-stretching region shows strong similarity between the three minerals. In the IR spectra, complexity exists with multiple antisymmetric stretching vibrations observed, due to the reduced tetrahedral symmetry. This loss of degeneracy is also reflected in the bending modes. Strong IR bands around 800 cm−1 are attributed to water librational modes. The spectra of the three minerals display similarities due to their compositions and crystal structures, but sufficient subtle differences exist for the spectra to be useful in distinguishing the species.

scholarly journals IR-Spectroscopic Study of Complex Formation of Nitrogen Oxides (NO, N2O) with Cationic Forms of Zeolites and the Reactivity of Adsorbed Species in CO and CH4 Oxidation

Molecules ◽  
2021 ◽  
Vol 27 (1) ◽  
pp. 55
Author(s):  
Alexander L. Kustov ◽  
Leonid M. Kustov
Keyword(s):  
Nitrogen Oxides ◽  
Molecular Form ◽  
Specific Geometry ◽  
Adsorption Of Co ◽  
Stretching Vibrations ◽  
Charge And Radius ◽  
Combination Bands ◽  
Ir Spectroscopic ◽  
Ir Bands ◽  
Formation Of Complexes

The formation of complexes and disproportionation of nitrogen oxides (NO, N2O) on cationic forms of LTA, FAU, and MOR zeolites was investigated by diffuse-reflectance IR spectroscopy. N2O is adsorbed on the samples under study in the molecular form and the frequencies of the first overtone of the stretching vibrations ν10–2 and the combination bands of the stretching vibrations with other vibrational modes for N2O complexes with cationic sites in zeolites (ν30–1 + ν10–1, ν10–1 + δ0–2) are more significantly influenced by the nature of the zeolite. The presence of several IR bands in the region of 2400–2600 cm−1 (the ν10–1 + δ0–2 transitions) for different zeolite types was explained by the availability of different localization sites for cations in these zeolites. The frequencies in this region also depend on the nature of the cation (its charge and radius). The data can be explained by the specific geometry of the N2O complex formed, presumably two-point adsorption of N2O on a cation and a neighboring oxygen atom of the framework. Adsorption of CO or CH4 on the samples with preliminarily adsorbed N2O at 20–180 °C does not result in any oxidation of these molecules. NO+ and N2O3 species formed by disproportionation of NO are capable of oxidizing CO and CH4 molecules to CO2, whereas NOx is reduced simultaneously to N2 or N2O. The peculiarities in the behavior of cationic forms of different zeolites with respect to adsorbed nitrogen oxides determined by different density and localization of cations have been established.

Schwingungsspektren und Normalkoordinatenanalyse der heteroleptischen Halogenohexaborate B6XnY6-n2-, n = 1-5; Χ ≠ Υ = Cl, Br, I / Vibrational Spectra and Normal Coordinate Analysis of the Heteroleptic Halogenohexaborates B6XnY6-n2-, n = 1— 5; Χ ≠ Y = Cl, Br, I

1991 ◽  
Vol 46 (5) ◽  
pp. 602-608 ◽  
Author(s):  
J. Thesing ◽  
M. Stallbaum ◽  
W. Preetz
Keyword(s):  
Potential Energy Distribution ◽  
Site Symmetry ◽  
Geometric Isomers ◽  
Normal Coordinate ◽  
Vibrational Coupling ◽  
Valence Force Field ◽  
Stretching Vibrations ◽  
Ir And Raman ◽  
Ir Bands ◽  
Good Agreement

Normal coordinate analyses for the 24 mixed halogenohexaborates B6XnY6-n2-, n = 1—5, Χ ≠ Y = Cl, Br, I, including the pairs of geometric isomers for n = 2, 3, 4 have been performed, based on a general valence force field. Using the bond lengths and force constants for the homoleptic species B6X62-, which with respect to the B6 cage are weighted standardized, the calculated frequencies are in good agreement with observed IR and Raman bands. The boronhalogen stretching vibrations for symmetric molecular axes correspond with the Ra(IR) bands of the homoleptic compounds: ClB6Cl 327 (515), BrB6Br 207 (430), IB6I 152 (394) cm-1. As a characteristic feature the mixed halogeno clusters exhibit bands with nearly averaged frequencies from asymmetrical axes: ClB6Br 261 (487), ClB6I 227 (473), BrB6I 178 (409) cm-1. This complete vibrational coupling is confirmed by properly balanced potential energy distribution on BX and BY bonds. There is a slight influence of the different substituents on the internal modes of the B6 cage (pseudo-Oh), observed in the sequence A1g>T1u> Eg>T2g in the region 1220-740 cm-1. The bands are shifted about 100 cm-1 with increasing mass of halogen, broadened by boron isotopomers (max. 60 cm-1), and degenerate vibrations are split by lowered point and site symmetry up to 100 cm-1.

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Electron Density ◽  
Partition Coefficients ◽  
Dna Bases ◽  
Atomic Charges ◽  
Free Energies ◽  
Solvation Model ◽  
Minimal Basis ◽  
Methylated Dna ◽  
Implicit Solvation Model ◽  
Good Agreement

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>

SAMPL6 Octanol-Water Partition Coefficients from Alchemical Free Energy Calculations with MBIS Atomic Charges

2019 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Free Energy ◽  
Electron Density ◽  
Free Energy Calculations ◽  
Basis Set ◽  
Energetic Cost ◽  
Atomic Charges ◽  
Free Energies ◽  
Energy Calculations ◽  
Alchemical Free Energy ◽  
Alchemical Free Energy Calculations

In molecular modeling the description of the interactions between molecules forms the basis for a correct prediction of macroscopic observables. Here, we derive atomic charges from the implicitly polarized electron density of eleven molecules in the SAMPL6 challenge using the Hirshfeld-I and Minimal Basis Set Iterative Stockholder(MBIS) partitioning method. These atomic charges combined with other parameters in the GAFF force field and different water/octanol models were then used in alchemical free energy calculations to obtain hydration and solvation free energies, which after correction for the polarization cost, result in the blind prediction of the partition coefficient. From the tested partitioning methods and water models the S-MBIS atomic charges with the TIP3P water model presented the smallest deviation from the experiment. Conformational dependence of the free energies and the energetic cost associated with the polarization of the electron density are discussed.

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