scholarly journals Conformational and structural stability of the single molecule and hydrogen bonded clusters of para aminobenzoic acid in the gas and solution phases

CrystEngComm ◽  
2018 ◽  
Vol 20 (46) ◽  
pp. 7543-7555 ◽  
Author(s):  
Ian Rosbottom ◽  
Dimitrios Toroz ◽  
Robert B. Hammond ◽  
Kevin J. Roberts
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Structural Stability ◽  
Single Molecule ◽  
Building Blocks ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Aminobenzoic Acid ◽  
Cluster Stability ◽  
Hydrogen Bonded

The structures of α- and β-para aminobenzoic acid are deconstructed into their hydrogen bonding molecular structural building blocks, where they are analysed usingab initioquantum mechanical calculations of their conformation and cluster stability in solution.

scholarly journals Nanomechanics of negatively supercoiled diaminopurine-substituted DNA

2021 ◽  
Author(s):  
Domenico Salerno ◽  
Francesco Mantegazza ◽  
Valeria Cassina ◽  
Matteo Cristofalo ◽  
Qing Shao ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Single Molecule ◽  
Conformational Dynamics ◽  
Persistence Length ◽  
Base Stacking ◽  
Base Pairs ◽  
Left Handed ◽  
Negative Supercoiling ◽  
Mechanical Dynamics ◽  
Hydrogen Bonded

ABSTRACTSingle molecule experiments have demonstrated a progressive transition from a B- to an L-form helix as DNA is gently stretched and progressively unwound. Since the particular sequence of a DNA segment influences both base stacking and hydrogen bonding, the conformational dynamics of B-to-L transitions should be tunable. To test this idea, DNA with diaminopurine replacing adenine was synthesized to produce linear fragments with triply hydrogen-bonded A:T base pairs. Triple hydrogen bonding stiffened the DNA by 30% flexurally. In addition, DAP-substituted DNA formed plectonemes with larger gyres for both B- and L-form helices. Both unmodified and DAP-substituted DNA transitioned from a B- to an L-helix under physiological conditions of mild tension and unwinding. This transition avoids writhing by DNA stretched and unwound by enzymatic activity. The intramolecular nature and ease of this transition likely prevent cumbersome topological rearrangements in genomic DNA that would require topoisomerase activity to resolve. L-DNA displayed about tenfold lower persistence length indicating it is much more contractile and prone to sharp bends and kinks. However, left-handed DAP DNA was twice as stiff as unmodified L-DNA. Thus, significantly doubly and triply hydrogen bonded segments have very distinct mechanical dynamics at physiological levels of negative supercoiling and tension.

N2 positively charged defects in diamond. A quantum mechanical investigation of the structural, electronic, EPR and vibrational properties

2020 ◽  
Vol 8 (15) ◽  
pp. 5239-5247 ◽  
Author(s):  
Giulio Di Palma ◽  
Francesco Silvio Gentile ◽  
Valentina Lacivita ◽  
William C. Mackrodt ◽  
Mauro Causà ◽  
...  
Keyword(s):  
Ab Initio ◽  
Quantum Mechanical ◽  
Vibrational Properties ◽  
Quantum Mechanical Calculations ◽  
Mechanical Investigation ◽  
Crystal Code ◽  
Charged Defects ◽  
Positively Charged ◽  
Vibrational Characterization

Structural, EPR and vibrational characterization of the N2, N+2 and N++2 defects in diamond from ab initio quantum-mechanical calculations with the CRYSTAL code.

scholarly journals Hydrogen-bonding patterns in 2-amino-4,6-dimethoxypyrimidine–4-aminobenzoic acid (1/1)

2006 ◽  
Vol 62 (7) ◽  
pp. o2976-o2978 ◽  
Author(s):  
Kaliyaperumal Thanigaimani ◽  
Packianathan Thomas Muthiah ◽  
Daniel E. Lynch
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Carboxyl Group ◽  
Acid Molecule ◽  
Aminobenzoic Acid ◽  
Graph Set ◽  
Supramolecular Chain ◽  
Bonding Patterns ◽  
Hydrogen Bonded

In the title cocrystal, C6H9N3O2·C7H7NO2, the 2-amino-4,6-dimethoxypyrimidine molecule interacts with the carboxyl group of the 4-aminobenzoic acid molecule through N—H...O and O—H...N hydrogen bonds, forming a cyclic hydrogen-bonded motif [R 2 2(8)]. This motif further self-organizes through N—H...O hydrogen bonds to generate an array of six hydrogen bonds with the rings having the graph-set notation R 2 3(6), R 2 2(8), R 4 2(8), R 2 2(8) and R 2 3(6). The 4-aminobenzoic acid molecules self-assemble via N—H...O hydrogen bonds to form a supramolecular chain along the c axis.

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