Amide Bond Activation of Biological Molecules

Amide bonds are the most prevalent structures found in organic molecules and various biomolecules such as peptides, proteins, DNA, and RNA. The unique feature of amide bonds is their ability to form resonating structures, thus, they are highly stable and adopt particular three-dimensional structures, which, in turn, are responsible for their functions. The main focus of this review article is to report the methodologies for the activation of the unactivated amide bonds present in biomolecules, which includes the enzymatic approach, metal complexes, and non-metal based methods. This article also discusses some of the applications of amide bond activation approaches in the sequencing of proteins and the synthesis of peptide acids, esters, amides, and thioesters.

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3-D reconstruction of molecular shape from microcrystal thin sections

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100077311 ◽

1983 ◽

Vol 41 ◽

pp. 748-749

Author(s):

S. Cusack ◽

J.-C. Jésior

Keyword(s):

Three Dimensional ◽

Molecular Shape ◽

Biological Molecules ◽

Fourier Space ◽

Single Particles ◽

Thin Sections ◽

Standard Methods ◽

X Ray ◽

X Ray Crystallography ◽

Dimensional Reconstruction

Three-dimensional reconstruction techniques using electron microscopy have been principally developed for application to 2-D arrays (i.e. monolayers) of biological molecules and symmetrical single particles (e.g. helical viruses). However many biological molecules that crystallise form multilayered microcrystals which are unsuitable for study by either the standard methods of 3-D reconstruction or, because of their size, by X-ray crystallography. The grid sectioning technique enables a number of different projections of such microcrystals to be obtained in well defined directions (e.g. parallel to crystal axes) and poses the problem of how best these projections can be used to reconstruct the packing and shape of the molecules forming the microcrystal.Given sufficient projections there may be enough information to do a crystallographic reconstruction in Fourier space. We however have considered the situation where only a limited number of projections are available, as for example in the case of catalase platelets where three orthogonal and two diagonal projections have been obtained (Fig. 1).

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Imine as a Linchpin Approach for Distal C(sp2)–H Functionalization

10.26434/chemrxiv.11521827 ◽

2020 ◽

Author(s):

Sukdev Bag ◽

Sadhan Jana ◽

Sukumar Pradhan ◽

Suman Bhowmick ◽

Nupur Goswami ◽

...

Keyword(s):

Organic Molecules ◽

Bond Activation ◽

Bond Formation ◽

Ancillary Ligand ◽

Significant Challenge ◽

Site Selectivity ◽

Directing Group ◽

Covalently Linked ◽

Complex Organic ◽

Post Functionalization

Despite the widespread applications of C–H functionalization, controlling site selectivity remains a significant challenge. Covalently attached directing group (DG) served as an ancillary ligand to ensure proximal ortho-, distal meta- and para-C-H functionalization over the last two decades. These covalently linked DGs necessitate two extra steps for a single C–H functionalization: introduction of DG prior to C–H activation and removal of DG post-functionalization. We introduce here a transient directing group for distal C(sp2)-H functionalization via reversible imine formation. By overruling facile proximal C-H bond activation by imine-N atom, a suitably designed pyrimidine-based transient directing group (TDG) successfully delivered selective distal C-C bond formation. Application of this transient directing group strategy for streamlining the synthesis of complex organic molecules without any necessary pre-functionalization at the distal position has been explored.

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The functional vascular anatomy of the swine for research

Vascular ◽

10.1177/1708538121996500 ◽

2021 ◽

pp. 170853812199650

Author(s):

Joseph Edwards ◽

Hossam Abdou ◽

Neerav Patel ◽

Marta J Madurska ◽

Kelly Poe ◽

...

Keyword(s):

Translational Research ◽

Functional Anatomy ◽

Three Dimensional ◽

Vascular Anatomy ◽

Review Article ◽

Imaging Data ◽

Preclinical Research ◽

Iodinated Contrast ◽

Translational Research Program ◽

And Function

Objectives Swine ( Sus Scrofa) are utilized broadly in research settings, given similarities to human vessel size and function; however, there are some important differences for clinicians to understand in order to interpret and perform translational research. This review article uses angiograms acquired in the course of a translational research program to present a description of the functional anatomy of the swine. Methods Digital subtraction angiography and computed tomography angiography were obtained throughout the course of multiple studies utilizing power injection with iodinated contrast. Subtracted two-dimensional images and three-dimensional multiplanar reformations were utilized post image acquisition to create maximal intensity projections and three-dimensional renderings of using open-source software (OsiriX). These imaging data are presented along with vessel measurements for reference. Results An atlas highlighting swine vascular anatomy, with an emphasis on inter-species differences that may influence how studies are conducted and interpreted, was compiled. Conclusions Swine are utilized in broad-reaching fields for preclinical research. While many similarities between human and swine vasculature exist, there are important differences to consider when conducting and interpreting research. This review article highlights these differences and presents accompanying images to inform clinicians gaining experience in swine research.

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1,2,3-Triazoles as Biomimetics in Peptide Science

Molecules ◽

10.3390/molecules26102937 ◽

2021 ◽

Vol 26 (10) ◽

pp. 2937

Author(s):

Naima Agouram ◽

El Mestafa El Hadrami ◽

Abdeslem Bentama

Keyword(s):

Enzymatic Degradation ◽

Triazole Ring ◽

Biologically Active ◽

Amide Bond ◽

Biologically Relevant ◽

Amide Bonds ◽

Natural Peptides ◽

Mimicking Peptides ◽

Chemical Mediators

Natural peptides are an important class of chemical mediators, essential for most vital processes. What limits the potential of the use of peptides as drugs is their low bioavailability and enzymatic degradation in vivo. To overcome this limitation, the development of new molecules mimicking peptides is of great importance for the development of new biologically active molecules. Therefore, replacing the amide bond in a peptide with a heterocyclic bioisostere, such as the 1,2,3-triazole ring, can be considered an effective solution for the synthesis of biologically relevant peptidomimetics. These 1,2,3-triazoles may have an interesting biological activity, because they behave as rigid link units, which can mimic the electronic properties of amide bonds and show bioisosteric effects. Additionally, triazole can be used as a linker moiety to link peptides to other functional groups.

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3D MR Neurography

Seminars in Musculoskeletal Radiology ◽

10.1055/s-0041-1730909 ◽

2021 ◽

Vol 25 (03) ◽

pp. 409-417

Author(s):

Omid Khalilzadeh ◽

Laura M. Fayad ◽

Shivani Ahlawat

Keyword(s):

Peripheral Nerves ◽

Tissue Characterization ◽

Three Dimensional ◽

Clinical Applications ◽

Review Article ◽

Mr Neurography ◽

Magnetic Resonance Neurography ◽

Technical Considerations ◽

Peripheral Nerve Diseases

AbstractHigh-resolution isotropic volumetric three-dimensional (3D) magnetic resonance neurography (MRN) techniques enable multiplanar depiction of peripheral nerves. In addition, 3D MRN provides anatomical and functional tissue characterization of different disease conditions affecting the peripheral nerves. In this review article, we summarize clinically relevant technical considerations of 3D MRN image acquisition and review clinical applications of 3D MRN to assess peripheral nerve diseases, such as entrapments, trauma, inflammatory or infectious neuropathies, and neoplasms.

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Electronic Effect on the Molecular Motion of Aromatic Amides: Combined Studies Using VT-NMR and Quantum Calculations

Molecules ◽

10.3390/molecules23092294 ◽

2018 ◽

Vol 23 (9) ◽

pp. 2294 ◽

Cited By ~ 2

Author(s):

Sungsoo Kim ◽

Jungyu Kim ◽

Jieun Kim ◽

Daeun Won ◽

Suk-Kyu Chang ◽

...

Keyword(s):

Aromatic Compounds ◽

Density Functional ◽

Electronic Effect ◽

Variable Temperature ◽

Rotational Barrier ◽

Amide Bond ◽

Theoretical Research ◽

Quantum Calculations ◽

Amide Bonds ◽

Barrier Energy

Rotational barrier energy studies to date have focused on the amide bond of aromatic compounds from a kinetic perspective using quantum calculations and nuclear magnetic resonance (NMR). These studies provide valuable information, not only regarding the basic conformational properties of amide bonds but also the molecular gear system, which has recently gained interest. Thus, we investigate the precise motion of the amide bonds of two aromatic compounds using an experimental rotational barrier energy estimation by NMR experiments and a theoretical evaluation of the density functional theory calculation. The theoretical potential energy surface scan method combined with the quadratic synchronous transit 3 method and consideration of additional functional group rotation with optimization and frequency calculations support the results of the variable temperature 1H NMR, with deviations of less than 1 kcal/mol. This detailed experimental and theoretical research strongly supports molecular gear motion in the aromatic amide system, and the difference in kinetic energy indicates that the electronic effect from the aromatic structure has a key role in conformational movements at different temperatures. Our study provides an enhanced basis for future amide structural dynamics research.

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Are the amide bonds in N-acyl imidazoles twisted? A combined solid-state 17O NMR, crystallographic, and computational study

Canadian Journal of Chemistry ◽

10.1139/cjc-2014-0397 ◽

2015 ◽

Vol 93 (4) ◽

pp. 451-458 ◽

Cited By ~ 7

Author(s):

Xianqi Kong ◽

Aaron Tang ◽

Ruiyao Wang ◽

Eric Ye ◽

Victor Terskikh ◽

...

Keyword(s):

Solid State ◽

Chemical Shift ◽

Crystal Structures ◽

Computational Study ◽

Chemical Shifts ◽

Amide Bond ◽

Chemical Shift Tensors ◽

Amide Bonds ◽

Bond Rotation ◽

Quadrupole Coupling

We report synthesis of 17O-labeling and solid-state 17O NMR measurements of three N-acyl imidazoles of the type R-C(17O)-Im: R = p-methoxycinnamoyl (MCA-Im), R = 4-(dimethylamino)benzoyl (DAB-Im), and R = 2,4,6-trimethylbenzoyl (TMB-Im). Solid-state 17O NMR experiments allowed us to determine for the first time the 17O quadrupole coupling and chemical shift tensors in this class of organic compounds. We also determined the crystal structures of these compounds using single-crystal X-ray diffraction. The crystal structures show that, while the C(O)–N amide bond in DAB-Im exhibits a small twist, those in MCA-Im and TMB-Im are essentially planar. We found that, in these N-acyl imidazoles, the 17O quadrupole coupling and chemical shift tensors depend critically on the torsion angle between the conjugated acyl group and the C(O)–N amide plane. The computational results from a plane-wave DFT approach, which takes into consideration the entire crystal lattice, are in excellent agreement with the experimental solid-state 17O NMR results. Quantum chemical computations also show that the dependence of 17O NMR parameters on the Ar–C(O) bond rotation is very similar to that previously observed for the C(O)–N bond rotation in twisted amides. We conclude that one should be cautious in linking the observed NMR chemical shifts only to the twist of the C(O)–N amide bond.

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Computer Aided Design of a Pattern and Risers for Casting Processes: Part 1

Journal of Engineering for Industry ◽

10.1115/1.2899623 ◽

1991 ◽

Vol 113 (1) ◽

pp. 59-66

Author(s):

Jong Cheon Park ◽

Kunwoo Lee

Keyword(s):

Computer Aided Design ◽

Unique Feature ◽

Three Dimensional ◽

Automatic Design ◽

Dimensional Model ◽

Three Dimensional Model ◽

High Quality ◽

Commercial Practice ◽

Interactive Computer Program ◽

Aided Design

An interactive computer program has been developed to design a pattern and risers for the production of castings of high quality. In our system, the user models the shape of a final product by using the system’s modeling capability, a pattern is generated in a three-dimensional model by eliminating the holes and adding shrinkage allowances and drafts, the proper riser is created automatically, and they are united together to yield a three-dimensional model of this portion of a mold assembly. The mold can be completed after the runners and the gating systems are designed, modeled, and united which will be described in Part 2 of this work. The unique feature of this work is a realization of an automatic design of the pattern and risers by integrating the modeling capabilities and the design equations used in commercial practice.

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Prebiologically Important Interstellar Molecules

Symposium - International Astronomical Union ◽

10.1017/s0074180900193246 ◽

2004 ◽

Vol 213 ◽

pp. 185-188

Author(s):

Y.-J. Kuan ◽

H.-C. Huang ◽

S. B. Charnley ◽

W.-L. Tseng ◽

L. E. Snyder ◽

...

Keyword(s):

Amino Acid ◽

Organic Molecules ◽

Prebiotic Chemistry ◽

Interstellar Space ◽

Central Question ◽

Dna And Rna ◽

The Galaxy ◽

Molecular Complexity ◽

Cloud Cores ◽

Complex Organic

Understanding the organic chemistry of molecular clouds, particularly the formation of biologically important molecules, is fundamental to the study of the processes which lead to the origin, evolution and distribution of life in the Galaxy. Determining the level of molecular complexity attainable in the clouds, and the nature of the complex organic material available to protostellar disks and the planetary systems that form from them, requires an understanding of the possible chemical pathways and is therefore a central question in astrochemistry. We have thus searched for prebiologically important molecules in the hot molecular cloud cores: Sgr B2(N-LMH), W51 e1/e2 and Orion-KL. Among the molecules searched: Pyrimidine is the unsubstituted ring analogue for three of the DNA and RNA bases. 2H-Azirine and Aziridine are azaheterocyclic compounds. And Glycine is the simplest amino acid. Detections of these interstellar organic molecular species will thus have important implications for Astrobiology. Our preliminary results indicate a tentative detection of interstellar glycine. If confirmed, this will be the first detection of an amino acid in interstellar space and will greatly strengthen the thesis that interstellar organic molecules could have played a pivotal role in the prebiotic chemistry of the early Earth.

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Ordered Assembling of Size and Shape Selected Nanocrystals

Microscopy and Microanalysis ◽

10.1017/s143192760002376x ◽

1998 ◽

Vol 4 (S2) ◽

pp. 728-729

Author(s):

Z.L. Wang

Keyword(s):

Organic Molecules ◽

Three Dimensional ◽

Building Blocks ◽

Organic Coating ◽

Self Organization ◽

Functional Specificity ◽

Orientation Order ◽

Self Assembled ◽

Superlattice Structures ◽

Physical And Chemical

Nanoparticles and the physical and chemical functional specificity and selectivity they possess, suggest them as ideal building blocks for two- and three-dimensional cluster self-assembled superlattice structures, in which the particles behave as well-defined molecular matter and they are arranged with long-range translation and even orientation order [1]. Self-assembled arrays involve self-organization into monolayers, thin films, and superlattices of size-selected nanoclusters encapsulated in protective compact organic coating. The macroscopic properties of the nanocrystal superlattice (NCS) are determined not only by the properties of each individual particle but by the coupling/interaction between nanocrystals interconnected and isolated by a monolayer of thin organic molecules.Periodic packing of nanocrystals is different from the 3-D packing of atoms. First, to an excellent approximation atoms are spherical, while nanoparticles can be faceted polyhedra, thus, the 3-D packing of particles can be critically affected by their shapes and sizes.

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