Managing the solvent water polarization to obtain improved NMR spectra of large molecular structures

The apparent acidity constant of p-hydroxybenzophenone, which is a practically insoluble drug in water but of great pharmaceutical interest, was determined by reversed-phase high-performance liquid chromatography in organic solvent – water mixtures (acetonitrile–water, ethanol–water, and methanol–water), varying the reaction medium permittivity in the interval 56 to 70, at constant ionic strength (0.050) and temperature (30 °C). A combined glass electrode calibrated with aqueous standard buffers was used to obtain pH readings based on the concentration scale (swpH). The pKa values from chromatographic data were obtained using the Hardcastle–Jano equation. Moreover, excellent linear relationships between the pKa values and solvation properties of the reaction medium (relative permittivity and Acity) were used to derive acid dissociation constants in aqueous solution. It has been concluded that the pKa values extrapolated from such solvent–water mixtures are consistent with each other and with previously reported measurements. In addition, the molecular structures of all the chemical species involved in the acid–base dissociation equilibrium studied were calculated with a B3LYP/6–311++G(d,p) method that makes use of the polarizable continuum model (PCM). Taking into account the theoretical pKa values, the conclusions obtained match our experimental determinations.Key words: solvent effects, p-hydroxybenzophenone, acidity constant, solvation parameters, structure, DFT calculation.

Download Full-text

Molecular Structures from 1H NMR Spectra: Education Aided by Internet Programs

Journal of Chemical Education ◽

10.1021/ed084p556 ◽

2007 ◽

Vol 84 (3) ◽

pp. 556 ◽

Cited By ~ 9

Author(s):

Barbara Debska ◽

Barbara Guzowska-Swider

Keyword(s):

1H Nmr ◽

Nmr Spectra ◽

Molecular Structures ◽

1H Nmr Spectra

Download Full-text

Assigning NMR spectra of irregular RNAs by heuristic algorithms

Bulletin of the Polish Academy of Sciences Technical Sciences ◽

10.1515/bpasts-2015-0037 ◽

2015 ◽

Vol 63 (1) ◽

pp. 329-338

Author(s):

M. Szachniuk

Keyword(s):

Nmr Spectra ◽

Heuristic Algorithms ◽

Expert Knowledge ◽

Molecular Structures ◽

Peak Picking ◽

Rna Structures ◽

Processing Stage ◽

Signal Assignment ◽

Computer Aided Analysis ◽

Manual Assistance

Abstract Computer-aided analysis and preprocessing of spectral data is a prerequisite for any study of molecular structures by Nuclear Magnetic Resonance (NMR) spectroscopy. The data processing stage usually involves a considerable dedication of time and expert knowledge to cope with peak picking, resonance signal assignment and calculation of structure parameters. A significant part of the latter step is performed in an automated way. However, in peak picking and resonance assignment a multistage manual assistance is still essential. The work presented here is focused on the theoretical modeling and analyzing the assignment problem by applying heuristic approaches to the NMR spectra recorded for RNA structures containing irregular regions.

Download Full-text

Purine complexes of platinum: synthesis, nmr, and crystal and molecular structures of cis-chloro(caffeine)bis(triethylphosphine)platinum(II) fluoroborate and cis-bis(isocaffeine)bis(triethylphosphine)platinum (II) fluoroborate

Canadian Journal of Chemistry ◽

10.1139/v83-202 ◽

1983 ◽

Vol 61 (6) ◽

pp. 1132-1141 ◽

Cited By ~ 14

Author(s):

Gordon William Bushnell ◽

Roderick James Densmore ◽

Keith Roger Dixon ◽

Arthur Charles Ralfs

Keyword(s):

Crystal Structure ◽

Nmr Spectra ◽

Molecular Structures ◽

Platinum Drugs ◽

Orthorhombic Space Group ◽

Space Group ◽

Bond Lengths ◽

Antitumour Agents ◽

Crystal And Molecular Structures ◽

Square Planar

Synthesis and 31P nmr spectra of the complex cations, cis-[PtCl(L)(PEt3)2]+, L= theophylline, caffeine, or isocaffeine, and cis[Pt(isocaff)2(PEt3)2]2+ are reported. The crystal structure of cis-[PtCl(caffeine)(PEt3)2][BF4] is determined, space group [Formula: see text], a = 1.1766(6), b = 1.4428(5), c = 0.9002(4) nm, α = 97.28(4)°, β = 97.69(4)°, γ = 100.96(5)°, Dm = 1.649 g cm−1, the bond lengths are Pt—Cl= 233.4(4) pm, Pt—N = 215(1) pm, Pt—P = 225.4(5) pm (mean), and the residual R = 0.071. The crystal structure of cis-[Pt(isocaffeine)2(PEt3)2][BF4]2 is orthorhombic, space group Pbca, a = 2.317(3), b = 1.717(3), c = 2.130(3) nm, Dm = 1.574 g cm−3, with an opposing isocaffeine conformation, bond lengths Pt—N = 211(2) pm, Pt—P = 227.6(9) pm (mean), and R = 0.073. Both crystal structures contain approximately square planar Pt(II) coordination with the purine coordinated via an imidazole nitrogen. The structures are discussed as models for the possible involvement of [Formula: see text] chelation of guanine to platinum when platinum drugs act as antitumour agents, but there is no evidence that isocaffeine acts as an [Formula: see text] chelate.

Download Full-text

Formation of organosilicon compounds 117:1 C-brominated 1,3,5-trisilacyclohexanes and their reactions with BuLi

Canadian Journal of Chemistry ◽

10.1139/v00-035 ◽

2000 ◽

Vol 78 (11) ◽

pp. 1388-1395 ◽

Cited By ~ 4

Author(s):

G Fritz ◽

M Keuthen ◽

F Kirschner ◽

E Matern ◽

H Goesmann ◽

...

Keyword(s):

Nmr Spectra ◽

Molecular Structures ◽

Ring Closure ◽

Organosilicon Compounds ◽

Structure Investigation ◽

X Ray ◽

Nmr Data ◽

High Yields ◽

Subsequent Substitution ◽

Preparative Route

The photobromination of 1,1,3,3,5,5-hexamethyl-1,3,5-trisilacyclohexane (1) almost exclusively attacks CH2 groups and results in 2,2-dibromo-trisilacyclohexane (2) as well as 2,2,4,4-tetrabromo-trisilacyclohexane (3) in high yields. Starting from a mixture of C-brominated trisilacyclohexanes the isomeric 2,2,9-tribromo-1,3,3,5,5,8,8,10,10,13,13-undecamethyl-1,3,5,8,10,13-hexasilabicyclo[7.2.2]tridec-6-yne (6) had been obtained in very low yield in an attempt to establish a preparative route to adamantanes with a C4Si6 skeleton, i.e., with C bridgeheads and SiR2 bridges. By ICl-cleavage of a Simethyl bond in 2 and subsequent substitution with Br3CLi, the trisilacyclohexane 4 with functional groups in opposite positions of the ring can be obtained. Linking the step-by-step synthesized Cl-Me2Si-C=C-SiMe2-CH2-SiMe2-Ph to the CBr3 group of 4 results after HBr-cleavage of the SiPh bond in (ω-bromo-octynyl)-trisilacyclohexane (12). A ring closure of 12 would result in an isomeric hexasila bicyclo[7.2.2]tridec-6-yne. The compounds were characterized by 1H, 13C, and 29Si NMR spectra. Additionally, the molecular structures of 4 and 6 were confirmed by X-ray single crystal investigations.Key words: 1,1,3,3,5,5-hexamethyl-1,3,5-trisilacyclohexane, bromination, 2,2,9-tribromo-1,3,3,5,5,8,8,10,10,13,13-undecamethyl-1,3,5,8,10,13-hexasilabicyclo[7.2.2]tridec-6-yne, carbosilane synthesis, NMR data, crystal structure investigation.

Download Full-text

The effect of a paramagnetic metal ion within a molecule: comparison of the structurally identical paramagnetic [3,3-Fe(1,2-C2B9H11)2]− with the diamagnetic [3,3-Co(1,2-C2B9H11)2]− sandwich complexes

Dalton Transactions ◽

10.1039/c4dt03418j ◽

2015 ◽

Vol 44 (6) ◽

pp. 2809-2818 ◽

Cited By ~ 7

Author(s):

Ana M. Cioran ◽

Francesc Teixidor ◽

Clara Viñas

Keyword(s):

Metal Ion ◽

Nmr Spectra ◽

Molecular Structures ◽

Sandwich Complexes ◽

Paramagnetic Metal

Effects on the NMR spectra of a paramagnetic metal ion are clearly observed by comparing identical sandwich molecular structures of diamagnetic [3,3′-Co(1,2-C2B9H11)2]− with paramagnetic [3,3′-Fe(1,2-C2B9H11)2]−.

Download Full-text

From NMR Spectra to Molecular Structures and Conformation

Stereochemistry and Global Connectivity: The Legacy of Ernest L. Eliel Volume 2 - ACS Symposium Series ◽

10.1021/bk-2017-1258.ch010 ◽

2017 ◽

pp. 161-190

Author(s):

Alan E. Tonelli

Keyword(s):

Nmr Spectra ◽

Molecular Structures

Download Full-text

Synthesis and characterization of N-silylated, C1-symmetric benzamidinates of lithium, sodium, and tin(II)

Canadian Journal of Chemistry ◽

10.1139/v05-250 ◽

2006 ◽

Vol 84 (2) ◽

pp. 269-276 ◽

Cited By ~ 12

Author(s):

Floria Antolini ◽

Peter B Hitchcock ◽

Alexei V Khvostov ◽

Michael F Lappert

Keyword(s):

Nmr Spectra ◽

Alkali Metals ◽

Membered Ring ◽

Molecular Structures ◽

Synthesis And Characterization ◽

Neutral Ligand ◽

X Ray Diffraction ◽

X Ray ◽

Ligand Free

The synthesis and characterization of complexes obtained from the reactions between Li[N-t-Bu(SiMe3)] (A) or the sodium analogue Na[N-t-Bu(SiMe3)] (B) and the cyanoarene RCN (R = Ph or 4-MeOC6H4) are discussed. These are the THF adduct [Li{µ-cis-N(t-Bu)C(Ph)N(SiMe3)}(THF)]2 (1), the TMEDA adduct Li[N(t-Bu)C(Ph)N(SiMe3)](TMEDA) (2), the neutral ligand-free lithium benzamidinate Li[N(t-Bu)C(C6H4OMe-4)N(SiMe3)] (3), and the THF adduct Li[N(t-Bu)C(C6H4OMe-4)N(SiMe3)](THF) (3a). The preparation and structure of the crystalline compound [Na{µ-cis-N(t-Bu)C(Ph)N(SiMe3)}(OEt2)]2 (4) is described. From the lithium benzamidinate 1 and Sn(II) chloride the tin(II) complex [Sn{N(t-Bu)C(Ph)N(SiMe3)}2] (5) was obtained. The molecular structures of the crystalline compounds 1, 4, and 5 were established by X-ray diffraction. In 1 and 4 the benzamidinato ligand is both chelating and bridging, with the Me3Si-substituted nitrogen atom as the bridging site. The central planar (MN)2 four-membered ring is a rhombus in 1, with almost equal LiN bond lengths, whereas in 4 the bonds to Na(1) are significantly longer than those to Na(2). In 5, the ligand is N,N′-chelating. Key words: alkali metals, tin(II), benzamidinates, NMR spectra, X-ray structures.

Download Full-text

Structure and 13C MAR NMR spectra of various forms of isomeric methyl xylobiosides

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19893092 ◽

1989 ◽

Vol 54 (11) ◽

pp. 3092-3101

Author(s):

Jan Schraml ◽

Eva Petráková ◽

Ján Hirsch ◽

Raivo Teeaar ◽

Endel Lippmaa

Keyword(s):

Nmr Spectra ◽

Chemical Shifts ◽

Elementary Cell ◽

Molecular Structures ◽

Magic Angle ◽

Angle Rotation ◽

State Chemical ◽

Crystalline Forms ◽

Paramagnetic Shifts ◽

C Nmr

All so far known crystalline forms of all positional isomers of methyl β-D-xylopyranosyl-β-D-xylopyranoside were prepared and their high resolution 13C NMR spectra measured by the magic angle rotation (MAR) method using cross-polarization (CP). According to these spectra only two modifications of methyl 4-O-(β-D-xylopyranosyl)-β-D-xylopyranoside (modifications IVβ and IVγ) contain more than one molecule in the crystal elementary cell; in all other studied disaccharide samples all molecules are equivalent. The majority of carbon-13 chemical shifts could be assigned, at least partially, by a comparison with solution spectra. Some of the glycosidic carbons in the units with methyl aglycone (ring A) exhibit surprisingly large paramagnetic shifts with respect to the solution chemical shifts. Apparently, molecular structures at these sites in solids differ most from the average structures the molecules assume in the liquid phase. Assuming that solid state chemical shifts are affected also by similar factors as the shifts in solution, the methyl aglycone carbon chemical shifts indicate that the frozen conformation of the ring A in the solid is closer either to 1C4 conformation (modifications IIIα and II) or to 4C1 conformation (modification IVα) than are the respective equilibrium conformations in solution. Thermal analysis has proven, however, that the xylobioside forms with two nonequivalent molecules in the cell similarly as some other forms are indeed hydrates. Thus is shown that all the methyl xylobiosides are monomorphous, all the polymorphs are not true polymorphs but forms hydrated to a different extent.

Download Full-text