Biomedical subjects

T M Alam

Publications and source records attributed to T M Alam.

11 recordsLinked to original sources

PubMed2006

(1)H-(13)C INEPT MAS NMR correlation experiments with (1)H-(1)H mediated magnetization exchange to probe organization in lipid biomembranes.

Two-dimensional (1)H-(13)C INEPT MAS NMR experiments utilizing a (1)H-(1)H magnetization exchange mixing period are presented for characterization of lipid systems. The introduction of the exchange period allows for structural information to be obtained via (1)H-(1)H dipolar couplings but with (13)C chemical shift resolution. It is shown that utilizing a RFDR recoupling sequence with short mixing times in place of the more standard NOE cross-relaxation for magnetization exchange during the mixing period allowed for the identification and separation of close (1)H-(1)H dipolar contacts versus longer-range inter-molecular (1)H-(1)H dipolar cross-relaxation. These 2D INEPT experiments were used to address both intra- and inter-molecular contacts in lipid and lipid/cholesterol mixtures.

Carbon Isotopes↗

PubMed2004

Distribution effects on 1H double-quantum MAS NMR spectra.

The effect of a distribution in the (1)H-(1)H dipolar coupling on (1)H double-quantum (DQ) magic angle spinning (MAS) nuclear magnetic resonance (NMR) spinning sideband patterns is considered. In disordered or amorphous materials a distribution in the magnitude of the (1)H-(1)H dipolar coupling is a realistic possibility. Simulations of the (1)H DQ MAS NMR spinning sideband spectra were performed with the two-spin approximation. These simulations reveal that a dipolar coupling distribution can greatly affect the DQ spectral shape and behavior of the DQ build-up. The spectral line shapes are quantified by measurement of the relative intensities of the DQ sidebands. These variations in the (1)H DQ NMR spectra are evaluated as a function of the width of the dipolar coupling distribution. As an example, the experimental DQ spinning sideband spectrum for a hydrated polyoxoniobate containing 15 H(2)O molecules per hexaniobate cluster, are better simulated with a distribution of dipolar couplings opposed to a single coupling constant.

Computer Simulation↗

PubMed2001

Structural diversity of lithium neopentoxide compounds.

The reaction of LiN(SiMe(3))(2) with 1 equiv of HOCH(2)CMe(3) (HONep) in toluene led to the formation of [Li(mu3-ONep)](8) (1). The complex adopts a novel dual-edge fused hexagon-square prismatic structure with a C(2v) axis of rotation that relates the top and bottom eight-membered rings. Substituting the noncoordinating solvent toluene for a Lewis basic solvent (THF or py) led to the isolation of compounds of the general formula [Li(mu3)-ONep)](4)(solv)(3), where solv = THF (2) or py (3). The cube structures of 2 and 3 have one Li which is not solvated because of steric crowding of the ONep ligands. Multinuclear solid-state ((6)Li, (7)Li, and (13)C) MAS and solution-state ((1)H, (7)Li, and (13)C) NMR studies were undertaken to verify the identity of the bulk powder and to determine the solution behavior of these compounds.

Journal Article↗

PubMed2001

203,205Tl NMR studies of crystallographically characterized thallium alkoxides. X-ray Structures of [TI(OCH2CMe3)]4 and [TI(OAr)]infinity, where OAr = OC6H3(Me)2-2,6 and OC6H3(CHMe2)2-2,6.

[Tl(OCH2Me)]4 (1) was reacted with excess HOR to prepare a series of [Tl(OR)]n, where OR = OCHMe2 (2, n = 4), OCMe3 (3, n = 4), OCH2CMe3 (4, n = 4), OC6H3(Me)2-2,6 (5, n = infinity), and OC6H3(CHMe2)2-2,6 (6, n = infinity). Single-crystal X-ray diffraction experiments revealed that in the solid state the alkoxide-ligated compound 4 adopts a cubane structure, whereas the aryloxide derivatives, 5 and 6, formed polymeric chains. Compounds 1-6 were also characterized by 203,205Tl solution and 205Tl solid-state NMR spectroscopy. In solution it was determined that 1-4 retained the [Tl-O]4 cube structure, whereas the polymeric species 5 and 6 appeared to be fluxional. Variations in the solution and solid-state structures for the [Tl(OR)]4 cubes and polymeric [Tl(OAr)]infinity are influenced by the steric hindrance of the ligand. The acidity of the parent alcohol influences the degree of covalency at the Tl metal center, which is reflected in the 203,205Tl chemical shifts for 1-6.

Journal Article↗

PubMed2000

Structural diversity in solvated lithium aryloxides. Syntheses, characterization, and structures of [Li(OAr)(THF)x]n and [Li(OAr)(py)x]2 complexes where OAr = OC6H5, OC6H4(2-Me), OC6H3(2,6-(Me))2, OC6H4(2-Pr(i)), OC6H3(2,6-Pr(i)))2, OC6h4(2-Bu(t)), OC6H3(2,6-Bu(t)))2.

A series of sterically varied aryl alcohols H-OAr [OAr = OC6H5 (OPh), OC6H4(2-Me) (oMP), OC6H3(2,6-(Me))2 (DMP), OC6H4(2-Pr(i)) (oPP), OC6H3(2,6-(Pr(i)))2 (DIP), OC6H4(2-Bu(t)) (oBP), OC6H3(2,6-(Bu(t)))2 (DBP); Me = CH3, Pr(i) = CHMe2, and Bu(t) = CMe3] were reacted with LiN(SiMe3)2 in a Lewis basic solvent [tetrahydrofuran (THF) or pyridine (py)] to generate the appropriate "Li(OAr)(solv)x". In the presence of THF, the OPh derivative was previously identified as the hexagonal prismatic complex [Li(OPh)(THF)]6; however, the structure isolated from the above route proved to be the tetranuclear species [Li(OPh)(THF)]4 (1). The other "Li(OAr)(THF)x" products isolated were characterized by single-crystal X-ray diffraction as [Li(OAr)(THF)]4 [OAr = oMP (2), DMP (3), oPP (4)], [Li(DIP)(THF)]3 (5), [Li(oBP)(THF)2]2, (6), and [Li(DBP)(THF)]2, (7). The tetranuclear species (1-4) consist of symmetric cubes of alternating tetrahedral Li and pyramidal O atoms, with terminal THF solvent molecules bound to each metal center. The trinuclear species 5 consists of a six-membered ring of alternating trigonal planar Li and bridging O atoms, with one THF solvent molecule bound to each metal center. Compound 6 possesses two Li atoms that adopt tetrahedral geometries involving two bridging oBP and two terminal THF ligands. The structure of 7 was identical to the previously reported [Li(DBP)(THF)]2 species, but different unit cell parameters were observed. Compound 7 varies from 6 in that only one solvent molecule is bound to each Li metal center of 7 because of the steric bulk of the DBP ligand. In contrast to the structurally diverse THF adducts, when py was used as the solvent, the appropriate "Li(OAr)(py)x" complexes were isolated as [Li(OAr)(py)2]2 (OAr = OPh (8), oMP (9), DMP (10), oPP (11), DIP (12), oBP (13)) and [Li(DBP)(py)]2 (14). Compounds 8-13 adopt a dinuclear, edge-shared tetrahedral complex. For 14, because of the steric crowding of the DBP ligand, only one py is coordinated, yielding a dinuclear fused trigonal planar arrangement. Two additional structure types were also characterized for the DIP ligand: [Li(DIP)(H-DIP)(py)]2 (12b) and [Li2(DIP)2(py)3] (12c). Multinuclear (6,7Li and 13C) solid-state MAS NMR spectroscopic studies indicate that the bulk powder possesses several Li environments for "transitional ligands" of the THF complexes; however, the py adducts possess only one Li environment, which is consistent with the solid-state structures. Solution NMR studies indicate that "transitional" compounds of the THF precursors display multiple species in solution whereas the py adducts display only one lithium environment.

Journal Article↗

PubMed2000

Multivariate analysis and quantitation of (17)O-nuclear magnetic resonance in primary alcohol mixtures.

Multivariate techniques were used to address the quantification of (17)O-nuclear magnetic resonance (NMR) spectra for a series of primary alcohol mixtures. Due to highly overlapping resonances, quantitative spectral evaluation using standard integration and deconvolution techniques proved difficult. Multivariate evaluation of the (17)O-NMR spectral data obtained for 26 mixtures of five primary alcohols demonstrated that obtaining information about spectral overlap and interferences allowed the development of more accurate models. Initial partial least squares (PLS) models developed for the (17)O-NMR data collected from the primary alcohol mixtures resulted in very poor precision, with signal overlap between the different chemical species suspected of being the primary contributor to the error. To directly evaluate the question of spectral overlap in these alcohol mixtures, net analyte signal (NAS) analyses were performed. The NAS results indicate that alcohols with similar chain lengths produced severely overlapping (17)O-NMR resonances. Grouping the alcohols based on chain length allowed more accurate and robust calibration models to be developed.

1-Butanol↗

PubMed1993

Molecular dynamics in lipid bilayers. Anisotropic diffusion in an odd restoring potential.

Recent 2H nuclear magnetic resonance spin relaxation studies have questioned the influence of restoring potential parity on the description of lipid or molecular reorientational dynamics. In biomembranes the polar head groups of lipid and sterol constituents are expected to associate with the aqueous interface; therefore, realistic descriptions of molecular reorientation in bilayer systems should use an odd restoring potential. The multiexponential correlation functions and related spectral density functions for small-step anisotropic diffusion in a pseudo-restoring potential of the form U(beta) = -lambda cos beta are evaluated as a function of molecular ordering . From analysis of these results the single exponential approximation used in previous investigations is found to overestimate the decay rate at lower order, but is reliable for > 0.6. The exception to this trend is the decay constant for the G11 (omega; t) correlation function, which is not accurately portrayed by the first-order approximations. A second-order single exponential approximation is presented, and is shown to be equivalent to the weighted sum of the multidecay constants. In general, the potential parity is found to have only minor effects on the spin relaxation rates obtained to describe molecular reorientation in lipid bilayers.

Diffusion↗

PubMed1991

Deuterium NMR investigation of backbone dynamics in the synthetic oligonucleotide [d(CGCGAATTCGCG)]2.

Backbone dynamics in the [5',5"-2H2]2'-deoxythymidine labeled duplex dodecamer [d-(CGCGAAT*T*CGC)]2 have been investigated by solid-state 2H NMR. Quadrupolar echo line shapes, spin-lattice relaxation, and quadrupolar echo decay times were obtained over hydration levels ranging from W = 0.0 to 25.2 (moles of H2O/mole of nucleotide). Variation of the line shape with changing hydration level was analyzed by using models employed in previous investigations of dodecamer base and sugar dynamics. Both fast local motions and a slower helix motion were present within the oligonucleotide. The fast motion was modeled as a four-site libration whose amplitude increased with hydration level. The root mean square amplitude of this librational model was 2-6 degrees larger than the amplitude observed in either the furanose ring or base labeled material for the entire range of hydration levels investigated. The observed line shape was inconsistent with a rapid three-site trans-gauche isomerization. A slow motion about the helix axis was observed at low water levels and increased in rate and amplitude with hydration. This motional model is in agreement with previous oligonucleotide studies.

Base Sequence↗

PubMed1990

A solid-state deuterium NMR investigation of conformation and order in magnetically oriented [d(CGCGAATTCGCG)]2.

Solid-state deuterium NMR has been used to investigate the oriented liquid crystal phase of the hydrated oligonucleotide [d(CGCGAATTCGCG)]2. Previous investigations have shown that the helix axis is aligned perpendicular to the magnetic field, while at reduced temperatures motion about the helix axis is eliminated. Synthetic oligonucleotide samples incorporating different labeled nucleosides, [2"-2H]-2'-deoxyadenosine, [methyl-2H]thymidine, [8-2H]-2'-deoxyguanosine, and [8-2H]-2'-deoxyadenosine, permitted investigation of both the base and sugar conformation and ordering in the aligned phase. From line-shape analysis of the purine-labeled samples the orientation of the base C8 C-D bond with respect to the helix axis was determined to be theta = 90 degrees with a distribution of sigma total = 20 degrees, which is comparable to the orientation of theta = 90 degrees, sigma total = 15 degrees, with an oriented fraction P = 0.7 found for the C3 symmetry axis of the methyl-labeled dodecamer. The orientation of the sugar 2" C-D bond with respect to the helix axis is theta = 22 degrees with a distribution of sigma total = 15 degrees in agreement with the expected C2'-endo sugar conformation. The fraction of C3'-endo was also investigated and from analysis of line shape cannot exceed 20%. These results, though preliminary in nature, illustrate the application of this aligned phase for structural investigations.

Base Sequence↗

PubMed1990

Dynamics in synthetic oligonucleotides. A solid-state deuterium NMR study.

Solid-state 2H NMR spectroscopy was used to investigate dynamics in the [methyl-2H]thymidine-labeled oligonucleotide [d(CGCGAAT*T*CGCG)]2. Quadrupole echo line shapes, spin-lattice relaxation, and quadrupolar echo decay rates were investigated as a function of hydration W (moles of water/moles of nucleotide) between 0 and approximately 30. The amplitude of the base motion, modeled as a fast four-site libration, or diffusion in a cone, increased slightly with higher levels of hydration. A slower component of motion about the helix axis appears at W approximately 10 and increases in rate and amplitude, leading to the intermediate rate line shape observed at W approximately 21.

Deuterium↗

PubMed1989

DNA polymorphism among isolates from multiple sites of a patient with chronic herpes simplex virus, type 1 infection.

DNA polymorphisms among independent isolates of herpes simplex virus (HSV) type 1 were studied from a 7-year-old male patient with recurrent infections of the skin and internal organs. In the patient's serum, HSV antibodies could not be detected by complement fixation, enzyme-linked immunosorbent assay (ELISA), or neutralization tests. ELISA tests for the presence of antibodies to human immunodeficiency virus were also negative. One HSV isolate was obtained from mesenteric nodes biopsied in 1983; one from skin in 1984; and three (postmortem) from brain, lungs, and liver in 1985. Restriction enzymes Eco RI, Bgl II, Hind III, Kpn I, and Bam H1 digestion patterns of the five isolates were similar. However, Sal I digests of isolates from skin, mesenteric nodes, lungs, and liver showed variations that were distinct from that of the brain isolate. Although Sal I digests of skin, mesenteric nodes, lungs, and liver isolates share a common variation in lacking F and G, the liver isolate can be further differentiated because of the gain of a restriction site on the H fragment. Thus, the three distinct variants observed were the isolates from brain (variant 1); from skin, mesenteric nodes, and lungs (variant 2); and from liver (variant 3). The fragments involved in variations among these isolates (presence or absence of Sal, G and H) are from the unique short and long regions (invariable regions) of the genome and therefore do not show heterogeneity in size. The extent of variation among these isolates is less than that seen among epidemiologically unrelated strains, suggesting that they originated from a single infecting strain, probably the brain isolate.

Animals↗