Two-dimensional Solid State Research Articles

Large Scale Parallel DNA Detection by Two-Dimensional Solid-State Multipore Systems.

We describe a scalable device design of a dense array of multiple nanopores made from nanoscale semiconductor materials to detect and identify translocations of many biomolecules in a massively parallel detection scheme. We use molecular dynamics coupled to nanoscale device simulations to illustrate the ability of this device setup to uniquely identify DNA parallel translocations. We show that the transverse sheet currents along membranes are immune to the crosstalk effects arising from simultaneous translocations of biomolecules through multiple pores, due to their ability to sense only the local potential changes. We also show that electronic sensing across the nanopore membrane offers a higher detection resolution compared to ionic current blocking technique in a multipore setup, irrespective of the irregularities that occur while fabricating the nanopores in a two-dimensional membrane.

Segmental isotopic labeling of HIV-1 capsid protein assemblies for solid state NMR.

Recent studies of noncrystalline HIV-1 capsid protein (CA) assemblies by our laboratory and by Polenova and coworkers (Protein Sci 19:716-730, 2010; J Mol Biol 426:1109-1127, 2014; J Biol Chem 291:13098-13112, 2016; J Am Chem Soc 138:8538-8546, 2016; J Am Chem Soc 138:12029-12032, 2016; J Am Chem Soc 134:6455-6466, 2012; J Am Chem Soc 132:1976-1987, 2010; J Am Chem Soc 135:17793-17803, 2013; Proc Natl Acad Sci USA 112:14617-14622, 2015; J Am Chem Soc 138:14066-14075, 2016) have established the capability of solid state nuclear magnetic resonance (NMR) measurements to provide site-specific structural and dynamical information that is not available from other types of measurements. Nonetheless, the relatively high molecular weight of HIV-1 CA leads to congestion of solid state NMR spectra of fully isotopically labeled assemblies that has been an impediment to further progress. Here we describe an efficient protocol for production of segmentally labeled HIV-1 CA samples in which either the N-terminal domain (NTD) or the C-terminal domain (CTD) is uniformly 15N,13C-labeled. Segmental labeling is achieved by trans-splicing, using the DnaE split intein. Comparisons of two-dimensional solid state NMR spectra of fully labeled and segmentally labeled tubular CA assemblies show substantial improvements in spectral resolution. The molecular structure of HIV-1 assemblies is not significantly perturbed by the single Ser-to-Cys substitution that we introduce between NTD and CTD segments, as required for trans-splicing.

Structure of Amorphous Selenium by 2D 77 Se NMR Spectroscopy: An End to the Dilemma of Chain versus Ring.

Amorphous selenium, owing to its tremendous technological importance and perhaps to its chemical simplicity, has been studied for nearly a century and yet an unequivocal structural description of this material remains lacking to date. The primary controversy regarding the structure of amorphous Se relates to the relative fraction of Se atoms residing in ∞1Se chains versus in Se8 rings. Herein we present the results of a two-dimensional solid-state 77 Se nuclear magnetic resonance (NMR) spectroscopic study of the chain and ring crystalline allotropes of Se as well as of amorphous Se to unequivocally demonstrate that 1) the Se8 rings and the ∞1Se chains are characterized by their unique 77 Se NMR signatures and 2) the structure of amorphous Se consists exclusively of ∞1Se chains.

Solid State NMR Characterization of Ibuprofen:Nicotinamide Cocrystals and New Idea for Controlling Release of Drugs Embedded into Mesoporous Silica Particles.

Grinding and melting methods were employed for synthesis of pharmaceutical cocrystals formed by racemic (R/S) and entiomeric (S) ibuprofen (IBU) and nicotinamide (NA) as coformer. Obtained (R/S)-IBU:NA and (S)-IBU:NA cocrystals were fully characterized by means of advanced one- and two-dimensional solid state nuclear magnetic resonance (SS NMR) techniques with very fast magic angle spinning (MAS) at 60 kHz. The distinction in molecular packing and specific hydrogen bonding pattern was clearly recognized by analysis of 1H, 13C, and 15N spectra. It is concluded from these studies that both methods (grinding and melting) provide exactly the same, specific forms of cocrystals. Thermal solvent-free (TSF) approach was used for loading of (R/S)-IBU:NA and (S)-IBU:NA into the pores of MCM-41 mesoporous silica particle (MSP). The progress and efficiency of this process was analyzed by NMR spectroscopy. It has been confirmed that TSF method is an effective and safe technique of filling the MSP pores with active pharmaceutical ingredients (APIs). By analyzing the NMR results, it has been further proved that excess of IBU and NA components, which are not embedded into the pores during melting and cooling, crystallize on the MCM-41 walls preserving very specific arrangement, characteristic for crystalline samples. By investigating kinetic of release for (R/S)-IBU/MCM-41, (S)-IBU:NA/MCM-41, and (R/S)-IBU:NA/MCM-41 samples containing active components exclusively inside of the pores, it was revealed that release of IBU is much faster for the first of the samples compared to those containing IBU and NA inside the pores. The hypothesis that the rate of release of API can be controlled by specific composition of cocrystal embedded into the MSP pore was further supported by study of (R/S)-IBU:BA/MCM-41 sample with benzoic acid (BA) as coformer.

Two-dimensional solid state gaseous detector based on 10B layer for thermal and cold neutrons

Two-dimensional solid state gaseous detector for thermal and cold neutrons is created. The detector has active area of 128 x 128 mm2, 10B neutron converter, and gas chamber with thin windows. The resistive charge-division readout is applied to determine the neutron position. The detector was tested using W-Be photoneutron source at the Institute for Nuclear Research, Moscow. The detector efficiency is estimated as ∼4% at neutron wavelength λ = 1.82 Å and 8% at λ = 8 Å. The efficiency of the background detection was less than 10-5 of that for thermal neutrons. The resulting pulse height resolution and the spatial resolution are estimated as ∼15% and ∼2.5 mm, respectively.

Three pulse recoupling and phase jump matching

The paper describes a family of novel recoupling pulse sequences, called three pulse recoupling. These pulse sequences can be employed for both homonuclear and heteronuclear recoupling experiments and are robust to dispersion in chemical shifts and rf-inhomogeneity. These recoupling pulse sequences can be used in design of two-dimensional solid state NMR experiments that use powdered dephased antiphase coherence (γ preparation) to encode chemical shifts in the indirect dimension. Both components of this chemical shift encoded gamma-prepared states can be refocused into inphase coherence by a recoupling element. This helps to achieve sensitivity enhancement in 2D NMR experiments by quadrature detection.

Steric Crowding of the Turn Region Alters the Tertiary Fold of Amyloid-β18–35 and Makes It Soluble

Aβ self-assembles into parallel cross-β fibrillar aggregates, which is associated with Alzheimer's disease pathology. A central hairpin turn around residues 23-29 is a defining characteristic of Aβ in its aggregated state. Major biophysical properties of Aβ, including this turn, remain unaltered in the central fragment Aβ18-35. Here, we synthesize a single deletion mutant, ΔG25, with the aim of sterically hindering the hairpin turn in Aβ18-35. We find that the solubility of the peptide goes up by more than 20-fold. Although some oligomeric structures do form, solution state NMR spectroscopy shows that they have mostly random coil conformations. Fibrils ultimately form at a much higher concentration but have widths approximately twice that of Aβ18-35, suggesting an opening of the hairpin bend. Surprisingly, two-dimensional solid state NMR shows that the contact between Phe(19) and Leu(34) residues, observed in full-length Aβ and Aβ18-35, is still intact in these fibrils. This is possible if the monomers in the fibril are arranged in an antiparallel β-sheet conformation. Indeed, IR measurements, supported by tyrosine cross-linking experiments, provide a characteristic signature of the antiparallel β-sheet. We conclude that the self-assembly of Aβ is critically dependent on the hairpin turn and on the contact between the Phe(19) and Leu(34) regions, making them potentially sensitive targets for Alzheimer's therapeutics. Our results show the importance of specific conformations in an aggregation process thought to be primarily driven by nonspecific hydrophobic interactions.

Emergent topological excitations in a two-dimensional quantum spin system

We study the mechanism of decay of a topological (winding-number) excitation due to finite-size effects in a two-dimensional valence-bond solid state, realized in an $S=1/2$ spin model ($J$-$Q$ model) and studied using projector Monte Carlo simulations in the valence bond basis. A topological excitation with winding number $|W|>0$ contains domain walls, which are unstable due to the emergence of long valence bonds in the wave function, unlike in effective descriptions with the quantum dimer model. We find that the life time of the winding number in imaginary time diverges as a power of the system length $L$. The energy can be computed within this time (i.e., it converges toward a "quasi-eigenvalue" before the winding number decays) and agrees for large $L$ with the domain-wall energy computed in an open lattice with boundary modifications enforcing a domain wall. Constructing a simplified two-state model and using the imaginary-time behavior from the simulations as input, we find that the real-time decay rate out of the initial winding sector is exponentially small in $L$. Thus, the winding number rapidly becomes a well-defined conserved quantum number for large systems, supporting the conclusions reached by computing the energy quasi-eigenvalues. Including Heisenberg exchange interactions which brings the system to a quantum-critical point separating the valence-bond solid from an antiferromagnetic ground state (the putative "deconfined" quantum-critical point), we can also converge the domain wall energy here and find that it decays as a power-law of the system size. Thus, the winding number is an emergent quantum number also at the critical point, with all winding number sectors becoming degenerate in the thermodynamic limit. This supports the description of the critical point in terms of a U(1) gauge-field theory.

Amyloid-β Oligomers: Now for the Structure in the Membrane

Small oligomers of Amyloid-β (Aβ), rather than the mature fibrils, are suspected to initiate Alzheimer's disease (AD). The structures of these oligomers in the solution, and in the membrane phase, are expected to provide significant cues for addressing their toxicity. However, it is difficult to determine the structure of these peptides as they are transient, and only exist at low μM concentrations. We recently combined rapid fluorescence techniques with slower two-dimensional solid state NMR to obtain useful atomic-level information on their structure in the solution phase1,2. However, though membrane interaction is a necessary step for this extra-cellular peptide to be toxic3, their structure in the membrane phase remains elusive. We have developed a modified Surface Enhanced Raman Spectroscopy method which is able to probe the structure of membrane proteins at individual residue levels. Using this technique, we determine the region-wise structure of the membrane-active oligomers, and compare these with those determined by solid state NMR spectroscopy. We show that there are critical differences in the structure of the oligomers and the fibrils, even though they share the same gross molecular architecture. These differences may be the key to understanding.References1)Sarkar et al., Structure of Transient Amyloid-β Oligomers from Less-Toxic Fibrils in reggions Known to harbour Familial Alzhimer's Mutations, Angew Chem. Int. Ed. Engl. 2014, http://dx.doi.org/10.1002/anie.2012)Nag et al., A folding transition underlies the emergence of membrane affinity in amyloid-beta. Phys. Chem. Chem. Phys. 2013, 15, 19129-19133.3)Sarkar et al., Thermodynamically Stable Amyloid-β monomers have much lower membrane affinity than the small oligomers, Frontiers in Physiology, 2013, 4, 1-11

Intermediate Role of Gallium in Oxidic Glasses: Solid State NMR Structural Studies of the Ga2O3–NaPO3 System

A series of (NaPO3)1–x(Ga2O3)x glasses (0 ≤ x ≤ 0.35) prepared by conventional melt-quenching methods has been structurally characterized by various complementary high resolution one-dimensional and two-dimensional (2D) solid state magic angle spinning nuclear magnetic resonance (MAS NMR) techniques, which were validated by corresponding experiments on the crystalline model compounds GaPO4 (quartz) and Ga(PO3)3. Alloying NaPO3 glass by Ga2O3 results in a marked increase in the glass transition temperature, similar to the effect observed with Al2O3. At the atomic level, multiple phosphate species QnmGa (n = 0, 1, and 2; m = 0, 1, 2, and 3) can be observed. Here n denotes the number of P–O–P and m the number of P–O–Ga linkages, and (m + n ≤ 4). For resolved resonances, the value of n can be quantified by 2D J-resolved spectroscopy, refocused INADEQUATE, and a recently developed homonuclear dipolar recoupling method termed DQ-DRENAR (double-quantum based dipolar recoupling effects nuclear alignment reduction). Ga3+ is dominantly found in six-coordination in low-Ga glasses, whereas in glasses with x > 0.15, lower-coordinated Ga environments are increasingly favored. The connectivity between P and Ga can be assessed by heteronuclear 71Ga/31P dipolar recoupling experiments using 71Ga{31P} rotational echo double resonance (REDOR) and 31P {71Ga} rotational echo adiabatic passage double resonance (READPOR) techniques. Up to x = 0.25, the limiting composition where this is possible, the second coordination sphere of all the gallium atoms is fully dominated by phosphorus atoms. Above x = 0.25, 71Ga static and MAS NMR as well as REDOR experiments give clear spectroscopic evidence of Ga–O–Ga connectivity. 31P/23Na REDOR and REAPDOR results indicate that gallium has no dispersion effect on sodium ions in these glasses. They also indicate significant differences in the strength of dipolar interactions for distinct QnmGa species, consistent with bond valence considerations. On the basis of these results, a comprehensive structural model is developed. This model explains the compositional trend of the glass transition temperatures in terms of the concentration of bridging oxygen species (P–O–P, P–O–Ga, and Ga–O–Ga) in these glasses. The results provide new insights into the role of Ga2O3 as an intermediate oxide, with features of both network modifier and network former in oxide glasses.

Two-Dimensional Solid-State Topochemical Reactions of 10,12-Pentacosadiyn-1-ol Adsorbed on Graphite

The photoinduced topochemical reaction of the diacetylene (DA) compound 10,12-pentacosadiyn-1-ol in the two-dimensional (2D) crystal phase adsorbed on graphite was examined by scanning tunneling microscopy (STM). The reaction efficiency and the structure of the generated polydiacetylene depend on its polymorphic forms, i.e., the "herringbone" or the "parallel" monomer arrangements. The reaction efficiency of the herringbone arrangement is lower than that of the parallel arrangement because the distance R between the probable reactant acetylenic carbon atoms of the herringbone arrangement is longer than that of the parallel arrangement. However, the fact that polydiacetylenes form from the herringbone arrangement (R = 0.58 nm) is contrary to the geometric criteria for the polymerization of three-dimensional (3D) crystals (the reaction was only observed if R < 0.4 nm). The polymerization criterion for the 2D phase differs from that of the 3D phase. In addition, the STM cross-section profiles of the polydiacetylenes reveal that the "lifted-up" and "in-plane" conformations form from the parallel and herringbone arrangements, respectively.

Structure of the Transient, Membrane-Active Amyloid Beta Oligomers in Physiological Solutions Probed by a Combination of Fluorescence and Solid State NMR

Small oligomers of Aβ are suspected to initiate Alzheimer's disease (AD). However, their low concentration and transient nature under physiological conditions have thwarted efforts to determine their structure. Using time resolved FRET spectroscopy, we have recently shown that the monomers are relatively unstructured, and the aggregation process starts with the two terminals of the peptide coming closer in the small oligomers (n-mers with n<10)1. Here we develop a method which combines rapid fluorescence techniques with slower two-dimensional solid state NMR, and probe nascent Aβ40 oligomers which demonstrate an enhanced ability to attach to cell membranes compared to the monomers2. We find that the conformation of the two hydrophobic arms (residues 10-22 and 29-40) have already reached the conformation observed in the fibrils. However, the turn region (residues 23 to 28) and the N-terminal tail (residues 1-9) are strikingly different. Notably, majority of the Aβ mutants linked to familial AD map to these two regions, and toxicity modulators such as Zn++ affect the same region3. Our results provide specific structural targets for therapeutic strategies designed to modulate Aβ oligomers.Reference:1. S. Nag, B. Sarkar, M. Chandrakesan, R. Abhyankar, D. Bhowmik, M. Kombrabail, S. Dandekar, E. Lerner, E. Haas and S. Maiti, Physical chemistry chemical physics: PCCP, 2013.2. B. Sarkar, A.K.Das and S.Maiti, Front. Physiol. 2013, 4(84), 1-11.3. V.S.Mithu, B. Sarkar, D Bhowmik, M. Chandrakesan, S. Maiti and P.K.Madhu, Biophysics. J. 2011, 101, 2825.

Functional Single‐Layer Graphene Sheets from Aromatic Monolayers

Self-assembled monolayers of aromatic molecules on copper substrates can be converted into high-quality single-layer graphene using low-energy electron irradiation and subsequent annealing. This two-dimensional solid state transformation is characterized on the atomic scale and the physical and chemical properties of the formed graphene sheets are studied by complementary microscopic and spectroscopic techniques and by electrical transport measurements. As substrates, Cu(111) single crystals and the technologically relevant polycrystalline copper foils are successfully used.

二维固体激光阵列逆达曼光栅相干合束技术模拟研究

二维固体激光阵列逆达曼光栅相干合束技术模拟研究

Signal enhancement for the sensitivity-limited solid state NMR experiments using a continuous, non-uniform acquisition scheme

We describe a sampling scheme for the two-dimensional (2D) solid state NMR experiments, which can be readily applied to the sensitivity-limited samples. The sampling scheme utilizes continuous, non-uniform sampling profile for the indirect dimension, i.e. the acquisition number decreases as a function of the evolution time ( t1) in the indirect dimension. For a beta amyloid (Aβ) fibril sample, we observed overall 40–50% signal enhancement by measuring the cross peak volume, while the cross peak linewidths remained comparable to the linewidths obtained by regular sampling and processing strategies. Both the linear and Gaussian decay functions for the acquisition numbers result in similar percentage of increment in signal. In addition, we demonstrated that this sampling approach can be applied with different dipolar recoupling approaches such as radiofrequency assisted diffusion (RAD) and finite-pulse radio-frequency-driven recoupling (fpRFDR). This sampling scheme is especially suitable for the sensitivity-limited samples which require long signal averaging for each t1 point, for instance the biological membrane proteins where only a small fraction of the sample is isotopically labeled.

Recoupling in solid state NMR using γ prepared states and phase matching

The paper describes two-dimensional solid state NMR experiments that use powdered dephased antiphase coherence ( γ preparation) to encode chemical shifts in the indirect dimension. Both components of this chemical shift encoded gamma-prepared states can be refocused into inphase coherence by a recoupling element. This helps to achieve sensitivity enhancement in 2D NMR experiments by quadrature detection. The powder dependence of the gamma-prepared states allows for manipulating them by suitable insertion of delays in the recoupling periods. This helps to design experiments that suppress diagonal peaks in 2D spectra, leading to improved resolution. We describe some new phase modulated heteronuclear and homonuclear recoupling pulse sequences that simplify the implementation of the described experiments based on γ prepared states. Recoupling in the heteronuclear spin system is achieved by matching the difference in the amplitude of the sine/cosine modulated phase on the two rf-channels to the spinning frequency while maintaining the same power on the two rf-channels.

A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers

We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes the connections that relate one signal list to another. As output, MCASSIGN2 produces a high-scoring sequential assignment of the multidimensional signals, using a score function that rewards good connections (i.e., agreement between relevant sets of chemical shifts in different signal lists) and penalizes bad connections, unassigned signals, and assignment gaps. Examination of a set of high-scoring assignments from a large number of independent runs allows one to determine whether a unique assignment exists for the entire sequence or parts thereof. We demonstrate the MCSA algorithm using two-dimensional (2D) and three-dimensional (3D) solid state NMR spectra of several model protein samples (α-spectrin SH3 domain and protein G/B1 microcrystals, HET-s(218-289) fibrils), obtained with magic-angle spinning and standard polarization transfer techniques. The MCSA algorithm and MCASSIGN2 program can accommodate arbitrary combinations of NMR spectra with arbitrary dimensionality, and can therefore be applied in many areas of solid state and solution NMR.

Solid State NMR Spectroscopy as a Precise Tool for Assigning the Tautomeric Form and Proton Position in the Intramolecular Bridges of o-Hydroxy Schiff Bases

Two analogous Schiff bases, (S,E)-2-((1-hydroxy-3-methyl-1,1-diphenylbutan-2-ylimino)methyl)phenol (1) and (S,Z)-2-hydroxy-6-((1-hydroxy-3-methyl-1,1-diphenylbutan-2-ylamino)methylene)cyclohexa-2,4-dienone (2), exist in the solid state as phenol-imine and keto-amine tautomers, respectively. Their crystal structures were solved using the X-ray diffraction method. Sample 1 forms orthorhombic crystals of space group P2(1)2(1)2(1), while 2 forms monoclinic crystals of space group P2(1). In each sample, one molecule is in the asymmetric unit of the crystal structure. One-dimensional and two-dimensional solid state NMR techniques were used for structure assignment and for inspection of the (13)C and (15)N δ(ii) of the chemical shift tensor (CST) values. NMR study indicates that the span (Ω = δ(11)-δ(33)) and the skew (κ = 3(δ(22)-δ(iso)/Ω) are extremely sensitive to change in the tautomeric form of the Schiff bases. Theoretical calculations of NMR shielding parameters for 1 and 2 and a model compound with reduced aliphatic residue were performed using the GIAO method with B3LYP functional and 6-311++g(d,p) basis sets. From comparative analysis of the experimental and theoretical parameters, it was concluded that the position of hydrogen in the intramolecular bridge has tremendous influence on (13)C and (15)N CST parameters. Inspection of Ω and κ parameters allowed for the establishment of the nature of the hydrogen bonding and the assignment of the equilibrium proton position in the intramolecular bridges in the solid state.

Structural and dynamical characterization of tubular HIV‐1 capsid protein assemblies by solid state nuclear magnetic resonance and electron microscopy

The wild-type HIV-1 capsid protein (CA) self-assembles in vitro into tubular structures at high ionic strength. We report solid state nuclear magnetic resonance (NMR) and electron microscopy measurements on these tubular CA assemblies, which are believed to contain a triangular lattice of hexameric CA proteins that is similar or identical to the lattice of capsids in intact HIV-1. Mass-per-length values of CA assemblies determined by dark-field transmission electron microscopy indicate a variety of structures, ranging from single-wall tubes to multiwall tubes that approximate solid rods. Two-dimensional (2D) solid state (13)C--(13)C and (15)N--(13)C NMR spectra of uniformly (15)N,(13)C-labeled CA assemblies are highly congested, as expected for a 25.6 kDa protein in which nearly the entire amino acid sequence is immobilized. Solid state NMR spectra of partially labeled CA assemblies, expressed in 1,3-(13)C(2)-glycerol medium, are better resolved, allowing the identification of individual signals with line widths below 1 ppm. Comparison of crosspeak patterns in the experimental 2D spectra with simulated patterns based on solution NMR chemical shifts of the individual N-terminal (NTD) and C-terminal (CTD) domains indicates that NTD and CTD retain their individual structures upon self-assembly of full-length CA into tubes. 2D (1)H-(13)C NMR spectra of CA assemblies recorded under solution NMR conditions show relatively few signals, primarily from segments that link the alpha-helices of NTD and CTD and from the N- and C-terminal ends. Taken together, the data support the idea that CA assemblies contain a highly ordered 2D protein lattice in which the NTD and CTD structures are retained and largely immobilized.

Characterization of the Solubility and Solid-State Properties of Saccharin Salts of Fluoroquinolones

Saccharinates salts of the fluoroquinolone antibiotics norfloxacin, ciprofloxacin, ofloxacin, and enrofloxacin were obtained as pure crystalline anhydrous solids with sweet taste. The products were characterized by one- (13C) and two-dimensional (1H–13C) dimensions solid state Nuclear Magnetic Resonance and infrared spectroscopy showing ionic interactions between the saccharine amide and the fluoroquinolone piperazine. Several intermolecular bindings were also identified. Thermal behavior and powder X-ray diffraction provided complementary evidences of salt formation. The series of products showed improved properties with respect to water solubility. A solubility model was developed. These salts would be a good way forward to developing more suitable formulations of these APIs. © 2009 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 98:3788–3801, 2009