scholarly journals Porous Si Partially Filled with Water Molecules—Crystal Structure, Energy Bands and Optical Properties from First Principles

Nanomaterials ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 396
Author(s):  
Ya. Shchur ◽  
O. Pavlyuk ◽  
A.S. Andrushchak ◽  
S. Vitusevich ◽  
A.V. Kityk
Keyword(s):  
Optical Properties ◽  
Hydrogen Bonds ◽  
First Principles ◽  
Energy Band ◽  
Visible Range ◽  
Band Spectrum ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Porous Si ◽  
Oh Groups

The paper reports the results on first-principles investigation of energy band spectrum and optical properties of bulk and nanoporous silicon. We present the evolution of energy band-gap, refractive indices and extinction coefficients going from the bulk Si of cubic symmetry to porous Si with periodically ordered square-shaped pores of 7.34, 11.26 and 15.40 Å width. We consider two natural processes observed in practice, the hydroxylation of Si pores (introduction of OH groups into pores) and the penetration of water molecules into Si pores, as well as their impact on the electronic spectrum and optical properties of Si superstructures. The penetration of OH groups into the pores of the smallest 7.34 Å width causes a disintegration of hydroxyl groups and forms non-bonded protons which might be a reason for proton conductivity of porous Si. The porosity of silicon increases the extinction coefficient, k, in the visible range of the spectrum. The water structuring in pores of various diameters is analysed in detail. By using the bond valence sum approach we demonstrate that the types and geometry of most of hydrogen bonds created within the pores manifest a structural evolution from distorted hydrogen bonds inherent to small pores (∼7 Å) to typical hydrogen bonds observed by us in larger pores (∼15 Å) which are consistent with those observed in a wide database of inorganic crystals.

scholarly journals Water Adsorption Properties of Free and Dehydrated β-Cyclodextrin Studied by near Infrared Spectroscopy and Gravimetry

2016 ◽  
Vol 689 ◽  
pp. 143-147 ◽  
Author(s):  
Alfred A. Christy
Keyword(s):  
Hydrogen Bonds ◽  
Infrared Spectra ◽  
Water Adsorption ◽  
Near Infrared ◽  
Adsorption Properties ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Oh Groups ◽  
Near Infrared Spectra ◽  
Adsorption Of Water

β-cyclodextrin, like other carbohydrates has a tendency to adsorb water molecules and the properties are attributed to the hydroxyl groups in the molecules. β-cyclodextrin, the cyclic oligomer of glucose has a hydrophobic interior and hydrophilic exterior. The cyclic structure favours the formation of hydrogen bonds between the OH groups on the adjacent glucose units and affects the formation of hydrogen bonds with water molecules. The hydoxyl groups engaged in hydrogen bondings can be eliminated at high temperatures and the adsorption properties of the dehydrated β-cyclodextrin will depend on the new functional groups formed. The aim of the report is to discuss the issue of the water adsorption properties of free and dehydrated β-cyclodextrin. Dry β-cyclodextrin and dehydrated β-cyclodextrin at temperatures 250, 300 and 350 °C were allowed to adsorb water from a humidity controlled air environmennt and the evolving near infrared spectra were measured using a near infrared spectrometer equipped with a transflectance accessory. The near infrared spectra in the region 10,000-4000 cm-1 and their second and fourth derivative profiles were used in studying the variation in the adsorption characteristics of dehydrated β-cyclodextrin. The results of the analyses show that the adsorption of water by β-cyclodextrin decreses at 300 °C compared to 200 and 250 °C. Dehydration forms more of the ethereal type-O-bonds in the molecule and explains the decrease in the water molecular adsorption at higher dehydration temperatures.

Spectroscopic studies of vanadium biosorption on different types of carbohydrate biomass

2013 ◽  
Vol 91 (3) ◽  
pp. 186-195 ◽  
Author(s):  
Jousy García ◽  
Juan Carlos González ◽  
María Inés Frascaroli ◽  
Silvia García ◽  
Patricia Blanes ◽  
...  
Keyword(s):  
Metal Ion ◽  
Orange Peel ◽  
Spectroscopic Studies ◽  
Visible Range ◽  
Water Molecules ◽  
Main Process ◽  
Paramagnetic Resonance ◽  
Oh Groups ◽  
Surface Level ◽  
Different Types

The biosorption potential of different types of carbohydrate biomass is investigated to evaluate their application to purify water contaminated by vanadium in environmentally relevant oxidation states (VIV and VV). Spectroscopic studies were done by electron paramagnetic resonance (EPR), vanadium nuclear magnetic resonance (51V NMR), circular dichroism (CD), and electronic absorption in the visible range (vis). Both d-galacturonic and d-glucuronic acids are major components of plant cellular wall polysaccharides. The interaction of VIV with the model ligands d-galacturonic and d-glucuronic acids showed that complexation starts at low pH values (pH 3) and that carboxylate and sugar–OH groups, as well as water molecules, are involved in the coordination. At pH > 4.5, coordination promotes the sugar–OH deprotonation and new species form with the ligand chelating the metal ion via oxygen atoms of carboxylate and of adjacent sugar–O− donors. The studies with pectin and citric acid show the ability of both compounds to partially reduce VV to VIV in solution and the EPR parameters suggest coordination of carboxylate, sugar–OH, and water molecules. The interaction of VV with biomass from different sources shows that grapefruit, orange peel, and plane tree fruit are the most suitable candidates for the biosorption of vanadium. Studies with VV and grapefruit (or the grainless stalk of corn) indicate that the reduction takes place at the “surface” of the solid. EPR studies on the interaction of VIV with different carbohydrate biomass show their ability to complex high amounts of VIV. We propose that the biosorption mechanism, when the biomass is in contact with VV species, involves sorption, reduction, and retention at the surface level of VIV coordinated by oxygen donors of the biomass. When the interaction starts with VIV, the main process just involves the uptake of the metal ion at the surface level.

Redetermination of rifampicin pentahydrate revealing a zwitterionic form of the antibiotic

2012 ◽  
Vol 68 (5) ◽  
pp. o209-o212 ◽  
Author(s):  
Barbara Wicher ◽  
Krystian Pyta ◽  
Piotr Przybylski ◽  
Ewa Tykarska ◽  
Maria Gdaniec
Keyword(s):  
Molecular Structure ◽  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Amide Group ◽  
Water Molecules ◽  
Acta Cryst ◽  
Oh Groups ◽  
Zwitterionic Form ◽  
The Family

Rifampicin belongs to the family of naphthalenic ansamycin antibiotics. The first crystal structure of rifampicin in the form of the pentahydrate was reported in 1975 [Gadret, Goursolle, Leger & Colleter (1975).Acta Cryst.B31, 1454–1462] with the rifampicin molecule assumed to be neutral. Redetermination of this crystal structure now shows that one of the phenol –OH groups is deprotonated, with the proton transferred to a piperazine N atom, confirming earlier spectroscopic results that indicated a zwitterionic form for the molecule, namely (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-21-acetyloxy-6,9,17,19-tetrahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-8-[(E)-N-(4-methylpiperazin-4-ium-1-yl)formimidoyl]-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienimino)naphtho[2,1-b]furan-5-olate pentahydrate, C43H58N4O12·5H2O. The molecular structure of this antibiotic is stabilized by a system of four intramolecular O—H...O and N—H...N hydrogen bonds. Four of the symmetry-independent water molecules are arrangedviahydrogen bonds into helical chains extending along [100], whereas the fifth water molecule forms only one hydrogen bond, to the amide group O atom. The rifampicin molecules interactviaO—H...O hydrogen bonds, generating chains along [001]. Rifampicin pentahydrate is isostructural with recently reported rifampicin trihydrate methanol disolvate.

scholarly journals First principles DFT calculations of the optical properties of A4BX6 group crystals

2021 ◽  
Vol 22 (1) ◽  
pp. 117-122
Author(s):  
H. Ilchuk ◽  
M. Solovyov ◽  
I. Lopatynskyi ◽  
F. Honchar ◽  
F. Tsyupko
Keyword(s):  
Optical Properties ◽  
First Principles ◽  
Energy Band ◽  
Density Functional ◽  
Near Infrared ◽  
Infrared Region ◽  
Energy Structure ◽  
Generalized Gradient ◽  
Reflection Index ◽  
Functional Theory

The results of investigating of the electron band energy structure and optical properties of A4BX6 (Tl4HgI6 and Tl4CdI6) group crystals are presented. The energy band structures of Tl4HgI6 and Tl4CdI6 crystals are calculated from the first principles within generalized gradient approximation (GGA). The band structure and reflection index were calculated using a pseudopotential method in the framework of density functional theory. Optical absorption edge in Tl4HgI6 and Tl4CdI6 is formed by direct optical transitions. The spectral dependence of the reflection index was calculated on the basis of the energy band results with using the Kramers–Kronig method. The spectra show pronounced anisotropy in E||a(b) and E||c polarizations. It was found the anomalous by large values of the birefringence (Δn > 0.18 for Tl4HgI6 and Δn > 0.03 for Tl4CdI6) in the visible and near infrared region.

scholarly journals Crystal structure of di-μ-hydroxido-bis{aqua[ethyl (1,10-phenanthrolin-3-yl)phosphonato-κ2N,N′]copper(II)} heptahydrate

2018 ◽  
Vol 74 (12) ◽  
pp. 1751-1754
Author(s):  
Alexander Yu. Mitrofanov ◽  
Yoann Rousselin
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Title Compound ◽  
Binuclear Complex ◽  
Three Dimensional ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Pyramidal Geometry ◽  
Square Pyramidal Geometry

In the title compound, [Cu2(OH)2{C12H7N2(PO3C2H5)}2(H2O)2]·7H2O, two Cu2+cations are bridged by two hydroxide groups, forming a centrosymmetric binuclear complex. Each Cu2+cation is further coordinated by the N atoms of a bidentate ethyl (1,10-phenanthrolin-3-yl)phosphonate anion and a water molecule in a square-pyramidal geometry. In the crystal, a network of O—H...O hydrogen bonds involving the P(O)(O−)(OEt) groups, bridging hydroxyl groups, coordinated and uncoordinated water molecules generates a three-dimensional supramolecular structure. The ethyl group exhibits disorder and was modelled over three sites with occupancies of 0.455, 0.384 and 0.161.

Polyimide Electronic Structural and Optical Properties from First Principles Calculations

2011 ◽  
Vol 694 ◽  
pp. 597-601
Author(s):  
Jia Qi Lin ◽  
Jing Leng ◽  
Ming Hui Xia ◽  
Jun Hui Shi ◽  
Qing Guo Chi
Keyword(s):  
Optical Properties ◽  
Band Structure ◽  
Band Gap ◽  
First Principles ◽  
Energy Band ◽  
Spectral Characteristics ◽  
Energy Band Structure ◽  
First Principles Calculations ◽  
Structural And Optical Properties ◽  
The Relationship

The electronic structural and optical properties of Polyimide (PI) are studied by first principle method of density theory. It is shown that molecules orbit contribution of PI is derived from carbon 2p orbital and oxygen 2p orbital, respectively,and the band gap from the energy band structure is much smaller than that of the experimental value. It is also found that the band gap calculated from the absorption edge of absorption spectra is in agreement with the result of the energy band structure. Furthermore, the relationship between the formation of dielectric function peaks and other spectral characteristics is interpreted.

scholarly journals IR-spectroscopy of hydrogen bonding in wood: Picea abies.

2017 ◽  
Author(s):  
В.И. Иванов-Омский ◽  
С.М. Герасюта ◽  
Е.И. Иванова
Keyword(s):  
Hydrogen Bonds ◽  
Picea Abies ◽  
Low Frequency ◽  
Temperature Stability ◽  
Experimental Spectrum ◽  
Hydroxyl Groups ◽  
Absorption Bands ◽  
Oh Groups ◽  
Adult Trees ◽  
Before And After

Исследованы ИК-спектры древесины ели обыкновенной в области поглощения валентными колебаниями гидроксильных групп. Изучались как образцы естественной влажности, так и подвергнутые отжигу при 105 °С. Образцы для исследований отбирались из взрослого дерева ели обыкновенной (Picea abies) на высоте 2,5–3 м (возраст в районе спилов 25–30 лет). Из безcучковой зоны вырезались образцы в виде кубиков размером 3×3×3 см3, из которых непосредственно перед записью спектра изготовлялось пять тангенциальных микротомных срезов толщиной 80–100 мкм. Спектральный анализ проводился с помощью ИК-Фурье спектрометра ФСМ-1201 с разрешением 4 см–1. Показано, что реальная микроструктура ели не препятствует разделению рассеянного и поглощаемого излучений. Для характеристики длин и энергий водородных связей использованы известные корреляционные соотношения частот поглощения гидроксильными группами, охваченными водородными связями, с их длиной и энергией. C этой целью экспериментальный спектр в области поглощения ОН-группами аппроксимируется гауссовыми контурами, каждый из которых ассоциируется с определенной разновидностью Н-связи. Сдвиги частот подгоночных контуров относительно частоты ОН-группы, не охваченной Н-связью, использованы для оценки энергий и длин связей, а соотношение их площадей – для оценки их концентраций. Показано, что при термическом отжиге происходит выжигание низкочастотного крыла полосы поглощения ОН-групп. Приводится диаграмма распределения Н-связей по концентрациям до отжига и после. Показано, что при отжиге число наиболее сильных связей незначительно уменьшается, но их энергия уменьшается заметно. Судя по величине частоты эти полосы поглощения относятся к межмолекулярным связям, и уменьшение их энергии означает, что отжиг затрагивает в первую очередь именно эти связи. Самые слабые исчезают совсем. Детальное исследование этого явления позволит обосновать выбор предельных температур тепловой обработки древесины, не нарушающих ее механических свойств. Отмечается более высокая температурная стабильность внутримолекулярных связей с энергией ≈10 кДж/моль. Investigated the IR spectra of spruce wood in the area of absorption of the stretching vibrations of hydroxyl groups. Been studied, as samples with natural moisture, and subjected to annealing at S. Samples for research were collected from adult trees of Norway spruce (Picea abies) at a height of 2.5–3.0 m (age in the area of cut 25–30 years). From cleared areas were cut samples in the form of cubes of size 3×3×3 cm3, of which just before recording the spectrum produced 5 tangential microtome sections with a thickness of 80–100 nm. Spectral analysis was performed using IR-Fourier spectrometer FSM-1201 with a resolution of 4 cm–1. Shows that the real microstructure of spruce does not prevent the separation of scattered and absorbed radiation. For the characteristic lengths and energies of hydrogen bonds used are known from the literature correlation of the ratio between the frequency of absorption of hydroxyl groups covered by hydrogen bonds with their length and energy. To this end, the experimental spectrum in the region of absorption of OH-groups approximated by a Gaussian contours, each of which is associated with a certain kind of H-bonds. The frequency shifts fitting contours of the relative frequency of OH-groups not covered by the H-bond, is used to evaluate energies and bond lengths, and the ratio of their squares to estimate their concentrations. It is shown that under thermal annealing is burning low frequency wing of the absorption bands of OH-groups. A diagram of the distribution of H-bonds energy on concentrations presented before and after annealing. It is shown that annealing the strongest bonds is slightly decreasing, but their energy decreases significantly. The weakest disappear altogether. A detailed study of this phenomenon will allow us to justify the choice of limiting the temperature of the heat treatment of wood that do not violate its mechanical properties. Noteworthy higher temperature stability of intramolecular bonds with energies of ≈10 kJ/mol.

Hydrogen-bond network in cyclodecaamylose hydrate at 20 K; neutron diffraction study of novel structural motifs band-flip and kink in α-(1→4)-D-glucoside oligosaccharides

2001 ◽  
Vol 57 (6) ◽  
pp. 833-841 ◽  
Author(s):  
K. Imamura ◽  
O. Nimz ◽  
J. Jacob ◽  
D. Myles ◽  
S. A. Mason ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Diffraction Study ◽  
Structure Refinement ◽  
Neutron Diffraction Study ◽  
The Other ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Neutron Density ◽  
Asymmetric Unit

A single-crystal neutron diffraction study of cyclodecaamylose (CA10) was carried out at 20 K. CA10 crystallizes with 27.18 water molecules [(C6H10O5)10·27.18H2O] in space group C2 with unit-cell constants a = 29.31 (5), b = 9.976 (10), c = 19.34 (2) Å, β = 121.07 (2)°. The asymmetric unit contains a half molecule of CA10 and 13.59 water molecules, the other half being related by a crystallographic twofold rotation axis. All H atoms except two water H atoms could be located from difference neutron-density maps; structure refinement converged at R = 0.635. Two of the five CH2—O6 groups and one of the 15 O2, O3 hydroxyl groups of CA10 are twofold orientationally disordered. A total of 13.59 water molecules in the asymmetric unit are distributed over 23 positions; 20 of which are in the CA10 cavity, and the other three occupy intermolecular interstices. Of the 123 symmetry-independent hydrogen bonds, 25 (= 20%) are three-centered and 7 (= 6%) are four-centered. Water molecules and O—H groups of CA10 form an extended network with cooperative O—H...O—H...O—H hydrogen bonds. They are arranged in 11 polygons with three, four, five, six and eight O—H bonds and in homodromic, antidromic and heterodromic arrangements. Nine polygons are located within the cavity and the others are outside.

Opening and Narrowing of the Water H—O—H Angle by Hydrogen-Bonding Effects: Re-inspection of Neutron Diffraction Data

1998 ◽  
Vol 54 (4) ◽  
pp. 464-470 ◽  
Author(s):  
T. Steiner
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Secondary Effects ◽  
X Ray Diffraction ◽  
X Ray ◽  
Sample Average

For 71 water molecules donating two Ow—H...O hydrogen bonds, the correlation of the covalent H—O—H angle and the O...Ow...O angle is inspected from 49 well refined organic and organometallic neutron diffraction crystal structures. Compared to sample average, the water angle is opened for large and narrowed for small O...Ow...O angles. Notably, the H—O—H angle is widened compared with the gas phase value even for small O...Ow...O. Related behavior is observed for chloride anion acceptors. The correlation exhibits a considerable scatter which should not be interpreted as experimental inaccuracies, but as secondary effects. Possible secondary effects are multi-center hydrogen bonding and effects of coordination to the water O atom. In a comparative test, low-temperature X-ray diffraction data were shown to be completely unsuitable for this type of analysis. The dependence of the C—O—H angle on the C—O...O angle in hydrogen bonds donated by hydroxyl groups in carbohydrates is also shown.

scholarly journals NEW PYRIDINE-3-SULFONATO TIN (IV), ANTIMONY (III) AND (V) HALO ADDUCTS AND COMPLEXES: SYNTHESIS AND INFRARED STUDY

2019 ◽  
Vol 25 (1) ◽  
Author(s):  
GUEYE AÏSSATOU ◽  
BIRAME DIOP MOUHAMADOU ◽  
LIBASSE DIOP
Keyword(s):  
Hydrogen Bonds ◽  
Water Molecules ◽  
Infrared Study ◽  
Oh Groups ◽  
Supramolecular Architectures ◽  
Chelating Ligand ◽  
Discrete Structures ◽  
Infrared Data

Six new tin (IV), antimony (III) and antimony (V) adducts and complexes have been synthesized. Discrete structures were suggested on the basis of infrared data. Within the structures, the anion behaves as a bidentate, monochelating and monodentate, monodentate and tri O-chelating ligand. The environments around metallic centres are octahedral.<em> </em>Considering preamble of extra hydrogen bonds in compounds containing water molecules and/or OH groups, supramolecular architectures may be given rise.

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