scholarly journals Quantum-chemical modeling of hydrogen bonds in α-glycine

2019 ◽  
Vol 57 (1) ◽  
pp. 21-26
Author(s):  
Alyona A. Lysenok ◽  
◽  
Pavel A. Kalmykov ◽  
Nina I. Giricheva ◽  
Tatiana G. Volkova ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Hydrogen Atoms ◽  
Acceptor Interaction ◽  
Chemical Modeling ◽  
X Ray ◽  
Method Of Calculation ◽  
Donor Acceptor ◽  
Crystal Fragment ◽  
Stretching Vibrations ◽  
Oxygen Atoms

Quantum chemistry was used to simulate a fragment of α-glycine crystal consisting of 5 and 6 glycine molecules. The α-glycine crystal fragment model was constructed using X-ray diffraction data contained in the Cambridge Crystallographic Database (CCDC). Theoretical IR spectra were obtained. It was shown that in a fragment of a crystal, glycine molecules in zwitterionic form form N-H...O hydrogen bonds of different strength, which correspond to different frequencies of stretching vibrations νst (N-H) of the NH3+ group. Full optimization of glycine crystal fragments consisting of a small number of molecules, regardless of the method of calculation, leads to the agglomeration of the structure. The system forms the maximum possible number of the most durable hydrogen bonds, thereby lowering the overall energy of the system, which leads to disruption of the crystal structure of the fragment, distortion of the parameters of hydrogen bonds in the crystal, and, consequently, to an unsystematic shift in the frequencies of N-H vibrations. To avoid this process, further modeling was performed by partially optimizing the geometry of the crystal fragment, with the positions of heavy nitrogen atoms, carbon and oxygen atoms being fixed, and only the positions of hydrogen atoms involved in the formation of hydrogen bonds were varied. Using the DFT/B3LYP/6-311G** method, the energies of donor–acceptor interaction in a fragment of a crystal, as well as its oscillation frequencies, are calculated. The calculated frequencies are consistent with the three experimental frequencies in the indicated X-ray region. A comparison was made between the calculated and experimental frequencies of the stretching vibrations of the N-H group of the NH3+ group. According to the geometric characteristics of the HB and the energy of donor-acceptor interaction between the lone electron pairs of oxygen atoms and the *(N-H) loosening orbitals, it was found that the hydrogen bonds of N-H...O between molecules in one layer are stronger than between molecules in different layers of a crystal.

Carbacylamidophosphates: Synthethis and Structure of N,N'-Tetramethyl-NM-benzoylphosphoryltriamide and Dimorpholido-N-benzoylphosphorylamide

2000 ◽  
Vol 55 (6) ◽  
pp. 495-498 ◽  
Author(s):  
Katerina E. Gubina ◽  
Vladimir A. Ovchynnikov ◽  
Vladimir M. Amirkhanov ◽  
Viktor V. Skopenkoa ◽  
Oleg V. Shishkinb
Keyword(s):  
Nmr Spectroscopy ◽  
Hydrogen Bonds ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Sodium Salts ◽  
Space Group ◽  
X Ray ◽  
Centrosymmetric Dimers ◽  
Oxygen Atoms

N,N′-Tetramethyl-N"-benzoylphosphoryltriamide (I) and dimorpholido-N-benzoylphosphorylamide (II), and their sodium salts Nal, Nall were synthesized and characterized by means of IR and 1H, 31P NMR spectroscopy. The structures of I, II were determined by X-ray diffraction: I monoclinic, space group P2i/c with a = 10.162(3), b= 11.469(4), c = 12.286(4) Å , β = 94.04°, V = 1428.4(8) A 3, Z = 4, p(calcd) = 1.187 g/cm3; II monoclinic, space group C2/c with a = 15.503(4), b = 10.991(3), c = 22.000(6) Å, β = 106.39°, V = 3596.3(17) Å3, Z = 8, p(calcd.) = 1.253 g/cm3. The refinement of the structures converged at R = 0.0425 for I, and R = 0.068 for II. In both structures the molecules are connected into centrosymmetric dimers via hydrogen bonds formed by the phosphorylic oxygen atoms and hydrogen atoms of amide groups.

The structure of chromium potassium alum

1958 ◽  
Vol 246 (1244) ◽  
pp. 78-90 ◽  
Keyword(s):  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Water Molecule ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
Potassium Alum ◽  
X Ray ◽  
Single Crystal Study ◽  
Thermal Vibrations ◽  
Oxygen Atoms

A single-crystal study of chromium potassium alum has been made by neutron diffraction, thus completing the structure first indicated by the X-ray investigations of Lipson & Beevers (1935). Hydrogen bonds link the oxygen atoms within the water molecules to other oxygen atoms in the structure. In each case the angle HOH for a water molecule is about 106°, although this sometimes entails appreciable displacement of the hydrogen atoms from the direct O—O line. Large thermal vibrations of the oxygen atoms in the sulphate groups are noteworthy.

Structure of Bis(isobutylammonium) Selenite and its Sesquihydrate

2006 ◽  
Vol 61 (11) ◽  
pp. 1401-1405
Author(s):  
Maren Wiechoczek ◽  
Peter G. Jones
Keyword(s):  
Hydrogen Bonds ◽  
Layer Structure ◽  
Selenium Dioxide ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Layer Structures ◽  
Graph Set ◽  
Ray Methods ◽  
Oxygen Atoms

Isobutylammonium selenite and its sesquihydrate were obtained in low yields by reaction of selenium dioxide with the neat amine in the presence of small amounts of water. Both structures were determined by X-ray methods and proved to contain two independent formula units. In both cases, layer structures [(CH3)2CHCH2NH3]2[SeO3] are formed in which all NH hydrogen atoms act as single hydrogen bond donors, and all selenite oxygen atoms accept two hydrogen bonds. The layers contain six independent rings; the anhydrous substance has all rings of graph set R34 (10), whereas the sesquihydrate has two each of R44 (12), R24 (8) and R34 (10). The three independent water molecules of the sesquihydrate attach themselves to the layer structure by further classical hydrogen bonds to the selenite oxygen atoms.

Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

2021 ◽  
Vol 19 ◽  
Author(s):  
Kikuko Iida ◽  
Toyokazu Muto ◽  
Miyuki Kobayashi ◽  
Hiroaki Iitsuka ◽  
Kun Li ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Molecular Conformation ◽  
Weak Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Molecular Surface ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Classical Hydrogen Bond

Abstract: X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

Synthese und Kristallstrukturen einiger Tetramethylstibonium-Hydrogendicarboxylate / Synthesis and Crystal Structures of Some Tetramethylstibonium Hydrogendicarboxylates

1982 ◽  
Vol 37 (11) ◽  
pp. 1393-1401 ◽  
Author(s):  
Beatrix Milewski-Mahrla ◽  
Hubert Schmidbaur
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Spectroscopic Data ◽  
Molar Ratio ◽  
Ionic Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Carboxylate Oxygen ◽  
Donor Acceptor ◽  
New Compounds

Reactions of pentamethylantimony (CH3)5Sb with carboxylic acids in the molar ratio 1:2 afford one equivalent of methane and essentially quantitative yields of crystalline tetramothylstibonium hydrogendicarboxylates. Six new compounds of this series have been synthesized using benzoic, o-phthalic, salicylic, 4-ethoxy-salicylic, oxalic, and malic acid, and characterized by analytical and spectroscopic data. An ionic structure with strong hydrogen bonds in the anionic components is proposed.The crystal structures of the hydrogen-dibenzoato (1), hydrogen-ortho-plithalato (2) and 4-ethoxy-hydrogen-salicylate (3) were determined by single crystal X-ray diffraction. The compounds can be described as having ionic lattices with some donor-acceptor inter­actions between the stibonium centers and the carboxylate oxygen atoms. The anions are characterized by strong hydrogen bonds O...H...O. Thus, the (CH3)4Sb-tetrahedron in 1 is distorted by two benzoate oxygon atoms (at 304(2) and 340(2) pin). The cation in 2 is largely undistorted and the anion has a hydrogenphthalate hydrogen bond of d(O...H...O) = 232 pm. The cation-anion contact in 3 is as short as d(Sb-O) = 289 pm rendering the Sb atom pentacoordinate.

scholarly journals Light-Induced Sulfur Transport inside Single-Walled Carbon Nanotubes

Nanomaterials ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 818 ◽  
Author(s):  
Olga Sedelnikova ◽  
Olga Gurova ◽  
Anna Makarova ◽  
Anastasiya Fedorenko ◽  
Anton Nikolenko ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Functional Properties ◽  
Single Walled Carbon Nanotubes ◽  
Acceptor Interaction ◽  
Local Composition ◽  
X Ray ◽  
Single Walled Carbon ◽  
Before And After ◽  
Donor Acceptor ◽  
Walled Carbon Nanotubes

Filling of single-walled carbon nanotubes (SWCNTs) and extraction of the encapsulated species from their cavities are perspective treatments for tuning the functional properties of SWCNT-based materials. Here, we have investigated sulfur-modified SWCNTs synthesized by the ampoule method. The morphology and chemical states of carbon and sulfur were analyzed by transmission electron microscopy, Raman scattering, thermogravimetric analysis, X-ray photoelectron and near-edge X-ray absorption fine structure spectroscopies. Successful encapsulation of sulfur inside SWCNTs cavities was demonstrated. The peculiarities of interactions of SWCNTs with encapsulated and external sulfur species were analyzed in details. In particular, the donor–acceptor interaction between encapsulated sulfur and host SWCNT is experimentally demonstrated. The sulfur-filled SWCNTs were continuously irradiated in situ with polychromatic photon beam of high intensity. Comparison of X-ray spectra of the samples before and after the treatment revealed sulfur transport from the interior to the surface of SWCNTs bundles, in particular extraction of sulfur from the SWCNT cavity. These results show that the moderate heating of filled nanotubes could be used to de-encapsulate the guest species tuning the local composition, and hence, the functional properties of SWCNT-based materials.

Das 7,8-Benzo-5-chloro-1,4,4-trimethyl-1-aza-4-azonia-6,9-dioxa-5 λ5-phosphaspiro[4.4]nonanyl-Kation: Röntgenstrukturanalyse und temperaturabhängige 1H-NMR-Spektren: The 7, 8-Benzo-5-chloro-1,4,4-trimethyl-1-aza-4-azonia-6,9-dioxa-5 λ).5-phosphaspiro[4.4]nonanyl Cation: X-Ray Crystal Structure Determination and Variable 1H NMR Spectra

1992 ◽  
Vol 47 (6) ◽  
pp. 755-759 ◽  
Author(s):  
Thomas Kaukorat ◽  
Peter G. Jones ◽  
Reinhard Schmutzler
Keyword(s):  
Crystal Structure ◽  
1H Nmr ◽  
Nmr Spectra ◽  
Crystal Structure Analysis ◽  
Acceptor Interaction ◽  
Nmr Spectrum ◽  
X Ray ◽  
H Nmr ◽  
Trigonal Bipyramidal ◽  
Donor Acceptor

The 1H NMR spectrum of the spirophosphorane 3 at room temperature indicates dynamic behaviour of the cation. The low-temperature 1H NMR spectra of 3 exhibit two sets of doublets for the protons of the diastereotopic N(CH3)2 groups. The free enthalpy of activation for the dynamic process was determined (58.6 KJ/mole). In the reaction of 3 with sodium tetraphenylborate the crystalline compound, 4, involving the non-coordinating anion, [B(C6H5)4]-, was obtained. The X-ray crystal structure analysis of 4 reveals the presence of a five-membered ring, formally as a result of intramolecular donor-acceptor interaction between the nitrogen atom of the N(CH3)2 group and phosphorus. The geometry at phosphorus deviates somewhat from ideal trigonal bipyramidal.

Bindung von Metall-Ionen an Dipeptide: Struktur von Thallium(I)-(3-benzyl-6-carboxylatomethyl-2,5-diketopiperazin) / Binding of Metal Ions by Dipeptides: Structure of Thallium(I) 3-Benzyl-6-carboxylatomethyl-2,5-diketopiperazine

1992 ◽  
Vol 47 (7) ◽  
pp. 952-956
Author(s):  
P. Mikulcik ◽  
P. Bissinger ◽  
J. Riede ◽  
H. Schmidbaur
Keyword(s):  
Solid State ◽  
Nitrogen Atom ◽  
Hydrogen Bonds ◽  
Diffraction Analysis ◽  
Carbonyl Oxygen ◽  
State Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Crystalline Product ◽  
Oxygen Atoms

Ester cleavage of aspartame (L-α-aspartyl-L-phenylalanine methylester) (1), by equimolar quantities of thallium ethoxide is accompanied by intramolecular cyclisation to give thallium 3-benzyl-6-(carboxylatomethyl)-2,5-dioxopiperazine (2). The solid state structure of the crystalline product was determined by single-crystal X-ray diffraction analysis. The cations were found to form four short and four elongated contacts to seven oxygen atoms and one nitrogen atom of a total of six neighbouring 3-benzyl-6-(carboxylatomethyl)-2,5-dioxopiperazine anions. There are inter-anionic hydrogen bonds only between the imino groups and the carbonyl oxygen atoms (O3, O4), featuring a pattern similar to that found for cytosine-guanosine contacts in DNA.

The crystal and molecular structure of guanine hydrochloride dehydrate

1965 ◽  
Vol 288 (1414) ◽  
pp. 418-439 ◽  
Keyword(s):  
Hydrogen Bonds ◽  
Least Squares Method ◽  
Three Dimensional ◽  
Water Molecules ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Anisotropic Temperature ◽  
Chlorine Ions ◽  
Atomic Coordinates ◽  
Single Crystal Analysis

The structure of guanine hydrochloride monohydrate has been determined by X-ray single crystal analysis and the parameters (including anisotropic temperature vibrations) have been refined by the three-dimensional least squares method. The unit cell is monoclinic with a = 14.69 ± 0.01, b = 13.40 ± 0.01, c = 4.840 ± 0.005 Å; β = 93.8°± 0.1°; space group P 2 1 / a . For 1600 independent reflexions the final value of the agreement index R was 0.07 and the standard deviations of atomic coordinates are in the region of 0.0035 Å. Two guanine molecules are linked together by hydrogen bonds to form a centrosymmetrical dimer. The dimer is linked by hydrogen bonds to four water molecules which are then hydrogen bonded to two chlorine ions. It is shown that the guanine molecule has associated with it six centres of electron density corresponding to hydrogen atoms and it is therefore in the form (H guanine) + with protonation at the N 7 position.

scholarly journals Crystal structure oftrans-cyclohexane-1,2-diammonium chromate(VI) from synchrotron X-ray diffraction data

2016 ◽  
Vol 72 (12) ◽  
pp. 1872-1874
Author(s):  
Dohyun Moon ◽  
Jong-Ha Choi
Keyword(s):  
Hydrogen Bonds ◽  
Organic Cation ◽  
Chair Conformation ◽  
The Other ◽  
X Ray Diffraction ◽  
Hybrid Compound ◽  
Acceptor Interaction ◽  
X Ray ◽  
Compound C ◽  
Hydrogen Bonding Interactions

The structure of the title hybrid compound, (C6H16N2)[CrO4], has been determined from synchrotron data. The organic cation adopts a chair conformation. The inorganic CrO42−anion is slightly distorted owing to its involvement in N—H...O hydrogen-bonding interactions with neighbouringtrans-cyclohexane-1,2-diammonium cations, whereby the two Cr—O bonds to the O atoms acting as acceptor atoms for two hydrogen bonds are slightly longer than the other two Cr—O bonds for which only one acceptor interaction per O atom is observed. In the crystal, cations and anions are packed into layers parallel to (001), held together through the aforementioned N—H...O hydrogen bonds.

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