Steered molecular dynamics simulation study on dynamic self-assembly of single-stranded DNA with double-walled carbon nanotube and graphene

Cheng, Chang-Li; Zhao, G.

doi:10.1039/c2nr12112c

Cited by 56 publications

(41 citation statements)

References 38 publications

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“…By calculating the aforementioned excitation energy, we can conclude that the intermolecular hydrogen bonding was enhanced after the formation of the complex2. The relationship between the excited state hydrogen bonding dynamics and the IC process was first qualitatively demonstrated by Zhao [51][52][53][54][55][56]. The deactivation of the excited state via IC can be remarkably facilitated by the intermolecular hydrogen bonding interactions.…”

Section: Accepted Manuscriptmentioning

confidence: 97%

TDDFT study on recognition mechanism for the oxygen sensing of the cyclometalated platinum (II) complex

Tong

Zhao

et al. 2017

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

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Section: Accepted Manuscriptmentioning

confidence: 97%

TDDFT study on recognition mechanism for the oxygen sensing of the cyclometalated platinum (II) complex

Tong

Zhao

et al. 2017

Spectrochimica Acta Part A: Molecular and Biomolecular Spectros

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“…no net unfolding. [26] Recently, it has been widely applied for stretching of proteins [27,28] and unfolding of bio-macromolecules when they are passing through carbon tubes, [29,30] which accelerates the computation compared with conventional MD simulations. It is concluded that unlike the thermal effects, [24,25] successful simulations of proteins under high pressure depend on the size of the protein molecule and would be very time-consuming for relatively large molecules.…”

Section: Introductionmentioning

confidence: 99%

Insights of Pressure‐induced Unfolding of β‐Lactoglobulin as Revealed by Steered Molecular Dynamics

Zhang

et al. 2019

Advcd Theory and Sims

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High hydrostatic pressure (HHP) has been widely used in various industries, and the protein as one of the most noticeable bio-macromolecules has exhibited distinct structural and functional characteristics under HHP conditions. In this work, steered molecular dynamics (SMD) simulations of β-lactoglobulin (βlg) are exploited to investigate the flexibility of the individual secondary structural element of the polypeptide. The two loops and the two helices on the two sides of the molecular β-barrel are found to be highly flexible and migrate toward the hydrophobic interior of the protein at relatively low pressures. Interestingly, there is evidence illustrating that water penetrations only occur from the loop-side of the barrel under pressurizations, which is favored by the enlarged β-barrel induced through the loop compression. Moreover, increased stability of βlg is attributed to the rigid regions of the protein molecule. N-and C-termini of the polypeptide chain are also found to be of great importance to pressure-induced unfolding of βlg. It is found the modeling results agree with previous experimental observations, demonstrating the validity of the applications of SMD for studies on pressure-induced protein unfolding. Such methodology will provide new insight into HHP and be generalized for more complicated systems such as enzymes.

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“…Being widely recognized, the nature and law of the hydrogen bonding has become one of the contemporary research interests in chemical and biochemical areas. Important results on various properties of many hydrogen-bonded complexes have been obtained in a number of theoretical [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19] and experimental works, [20][21][22][23][24][25] which include their geometrical structures, electronic spectras, electrostatic potential (ESP maps), the energy changes of the intermolecular hydrogen bond upon electronic excitation, the self-assembly issues, [18,19] and its influence on the photophysical and photochemical properties of the hydrogen-bonded molecules. Specifically, intermolecular hydrogen bonds have been found to have significant influences on the photophysical properties of compounds including heterocyclic aromatic [26] and carbonyl groups.…”

Section: Introductionmentioning

confidence: 99%

TDDFT study on the excited‐state hydrogen bonding of N‐(2‐hydroxyethyl)‐1,8‐naphthalimide and N‐(3‐hydroxyethyl)‐1,8‐naphthalimide in methanol solution

Yang

et al. 2014

J of Physical Organic Chem

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The time‐dependent density functional theory method was performed to investigate the excited‐state hydrogen‐bonding dynamics of N‐(2‐hydroxyethyl)‐1,8‐naphthalimide (2a) and N‐(3‐hydroxyethyl)‐1,8‐naphthalimide (3a) in methanol (meoh) solution. The ground and excited‐state geometry optimizations, electronic excitation energies, and corresponding oscillation strengths of the low‐lying electronically excited states for the complexes 2a + 2meoh and 3a + 2meoh as well as their monomers 2a and 3a were calculated by density functional theory and time‐dependent density functional theory methods, respectively. We demonstrated that the three intermolecular hydrogen bonds of 2a + 2meoh and 3a + 2meoh are strengthened after excitation to the S1 state, and thus induce electronic spectral redshift. Moreover, the electronic excitation energies of the hydrogen‐bonded complexes in S1 state are correspondingly decreased compared with those of their corresponding monomer 2a and 3a. In addition, the intramolecular charge transfer of the S1 state for complexes 2a + 2meoh and 3a + 2meoh were theoretically investigated by analysis of molecular orbital. Copyright © 2014 John Wiley & Sons, Ltd.

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Steered molecular dynamics simulation study on dynamic self-assembly of single-stranded DNA with double-walled carbon nanotube and graphene

Cited by 56 publications

References 38 publications

TDDFT study on recognition mechanism for the oxygen sensing of the cyclometalated platinum (II) complex

TDDFT study on recognition mechanism for the oxygen sensing of the cyclometalated platinum (II) complex

Insights of Pressure‐induced Unfolding of β‐Lactoglobulin as Revealed by Steered Molecular Dynamics

TDDFT study on the excited‐state hydrogen bonding of N‐(2‐hydroxyethyl)‐1,8‐naphthalimide and N‐(3‐hydroxyethyl)‐1,8‐naphthalimide in methanol solution

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