Experimental (13C NMR, 1H NMR, FT-IR, single-crystal X-ray diffraction) and DFT studies on 3,4-bis(isoproylamino)cyclobut-3-ene-1,2-dione

Süleymanoğlu, Nevin; Ustabaş, Reşat; Alpaslan, Yelda Bingöl; Eyduran, Fatih; Özyürek, Cengiz; Ískeleli, Nazan Ocak

doi:10.1016/j.saa.2011.08.068

Cited by 5 publications

(3 citation statements)

References 38 publications

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“…Once the first amine-containing molecule is attached to 30, such as an amine-containing fluorophore or PEG group, the remaining alkoxy group can be displaced by an exposed lysine side chain on the surface of a protein, resulting in the attachment of a new molecular entity to the protein. Molecular properties calculated at the B3LYP/6-31G(d,p) level for the bis-squaramide, 3,4-bis(isoproylamino)cyclobut-3-ene-1,2dione, were reported to agree well with experimental values for the geometry, atomic charges, vibrational frequencies, absorption wavelengths, and the HOMO and LUMO energies [143]. For 1,2-dianilinosquairane, the B3LYP/6-311++G(d,p) level DFT calculations were found to be in agreement with various experimental properties for this compound [144].…”

Section: Additional Modification Reactionssupporting

confidence: 52%

Thermodynamic Overview of Bioconjugation Reactions Pertinent to Lysine and Cysteine Peptide and Protein Residues

Lopandic,

Merza,

Honek

2023

Compounds

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Bioconjugation reactions are critical to the modification of peptides and proteins, permitting the introduction of biophysical probes onto proteins as well as drugs for use in antibody-targeted medicines. A diverse set of chemical reagents can be employed in these circumstances to covalently label protein side chains, such as the amine moiety in the side chain of lysine and the thiol functionality in cysteine residues, two of the more frequently employed sites for modification. To provide researchers with a thermodynamic survey of the reaction of these residues with frequently employed chemical modification reagents as well as reactive cellular intermediates also known to modify proteins non-enzymatically, a theoretical investigation of the overall thermodynamics of models of these reactions was undertaken at the T1 and G3(MP2) thermochemical recipe levels (gas phase), the M06-2X/6-311+G(2df,2p)/B3LYP/6-31G(d) (gas and water phase), and the M06-2X/cc-PVTZ(-f)++ density functional levels of theory (water phase). Discussions of the relationship between the reagent structure and the overall thermodynamics of amine or thiol modification are presented. Of additional interest are the observations that routine cellular intermediates such as certain thioesters, acyl phosphates, and acetyl-L-carnitine can contribute to non-enzymatic protein modifications. These reactions and representative click chemistry reactions were also investigated. The computational survey presented herein (>320 reaction computations were undertaken) should serve as a valuable resource for researchers undertaking protein bioconjugation. A concluding section addresses the ability of computation to provide predictions as to the potential for protein modification by new chemical entities, with a cautionary note on protein modification side reactions that may occur when employing synthetic substrates to measure enzyme kinetic activities.

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Section: Additional Modification Reactionssupporting

confidence: 52%

Thermodynamic Overview of Bioconjugation Reactions Pertinent to Lysine and Cysteine Peptide and Protein Residues

Lopandic,

Merza,

Honek

2023

Compounds

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“…First and foremost is the NMR spectroscopy , where a high‐frequency shift of the H‐atom signal along with increasing the associated 1 J (C,H) constants [5d] and heteronuclear Overhauser effect [5e] are an essential criteria for identification of C–H···X (X = O, N, S) H‐bonding. The IR spectroscopy and DFT calculations [5a,d] were also found to be very useful in the studies of weak C–H···X interactions. However, in those rare events when authors were concerned with the proposed C Ar –H···O bonds, their assumptions were based only on the data of 2 – 3 spectroscopic methods.…”

Section: Introductionmentioning

confidence: 99%

Experimental Evidence of Intramolecular C_Ar–H···O=C Hydrogen Bonds in the Structure of (Diaryl)tetrahydrofuranones Using Spectroscopic Tools

Semenok

Medvedev

Avdontceva

et al. 2016

Helvetica Chimica Acta

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The occurrence of bifurcate H‐bonds CAr–H···O=C in the structure of (diaryl)‐tetrahydrofuranones was experimentally demonstrated using different methods and techniques. The consistent increasing spin–spin coupling constants 1J(C,H) of the ortho‐H‐atoms and low‐field shift of vC=O in IR spectra of 2,2‐(diaryl)tetrahydrofuran‐3(2H)‐ones relative to their 5,5‐diaryl counterparts, as well as pronounced dependence of the ortho‐C–H H‐atoms chemical shifts on the temperature and solvent polarity along with X‐ray diffraction analysis data unambiguously point to the existence of weak CAr–H···O=C H‐bonds in these molecules.

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“…The frontier molecular orbitals (highest occupied molecular orbital-HOMO and lowest unoccupied molecular orbital-LUMO) of chemical species are of prime importance to describe chemical reactivity and stability. It is known that the HOMO-LUMO gap also is a critical parameter for electric, optical and other prosperities of molecular admittance, as well as in UV-Vis spectra and chemical reactions [16][17][18][19][20]. It can be easily seen that HOMO of the structures of 5, 6, and 7, are mainly on one benzene ring, whereas lowest unoccupied molecular orbital (LUMO) of the structures substantially localized on another benzene ring of title molecules.…”

Section: Synthesis Of 14-bis{(2-aminobenzoil) Amino}butane (7) and Imentioning

confidence: 99%

Nontemplate synthesis, characterization and theoretical study of tetraazamacrocycles

Șen¹,

Yildiz²,

Azizoğlu³

2012

Analele Universitatii "Ovidius" Constanta - Seria Chimie

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The syntheses of new tetraaza macrocyclic compounds of variable ring sizes by non-template methods and their characterization with the help of elemental analysis and spectroscopic techniques (FT-IR, 1H-NMR, and 13C-NMR) have been reported in detail. The vibrational frequencies determined experimentally are compared with those obtained theoretically from density functional theory (DFT) and Hartree-Fock (HF) calculations. The comparisons between the experimental and theoretical results indicate that B3LYP level with both the 3-21G(d) and 6-31G+(d,p) basis sets is able to provide satisfactory results for predicting IR properties. The frontier molecular orbital diagrams and molecular electrostatic potential maps of title compounds have been also calculated and visualized at the B3LYP/6-31G+(d,p) level of theory.

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Experimental (13C NMR, 1H NMR, FT-IR, single-crystal X-ray diffraction) and DFT studies on 3,4-bis(isoproylamino)cyclobut-3-ene-1,2-dione

Cited by 5 publications

References 38 publications

Thermodynamic Overview of Bioconjugation Reactions Pertinent to Lysine and Cysteine Peptide and Protein Residues

Thermodynamic Overview of Bioconjugation Reactions Pertinent to Lysine and Cysteine Peptide and Protein Residues

Experimental Evidence of Intramolecular C_Ar–H···O=C Hydrogen Bonds in the Structure of (Diaryl)tetrahydrofuranones Using Spectroscopic Tools

Nontemplate synthesis, characterization and theoretical study of tetraazamacrocycles

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Experimental (13C NMR, 1H NMR, FT-IR, single-crystal X-ray diffraction) and DFT studies on 3,4-bis(isoproylamino)cyclobut-3-ene-1,2-dione

Cited by 5 publications

References 38 publications

Thermodynamic Overview of Bioconjugation Reactions Pertinent to Lysine and Cysteine Peptide and Protein Residues

Thermodynamic Overview of Bioconjugation Reactions Pertinent to Lysine and Cysteine Peptide and Protein Residues

Experimental Evidence of Intramolecular CAr–H···O=C Hydrogen Bonds in the Structure of (Diaryl)tetrahydrofuranones Using Spectroscopic Tools

Nontemplate synthesis, characterization and theoretical study of tetraazamacrocycles

Contact Info

Product

Resources

About

Experimental Evidence of Intramolecular C_Ar–H···O=C Hydrogen Bonds in the Structure of (Diaryl)tetrahydrofuranones Using Spectroscopic Tools