Calculating free energies of organic molecules on insulating substrates

• Julian Gaberle,
• David Z. Gao and
• Alexander L. Shluger

Beilstein J. Nanotechnol. 2017, 8, 667–674, doi:10.3762/bjnano.8.71

• trajectories are finite and it is difficult to determine how long such simulations need to be. Attempts to compute free energies have been made for, i.e., proteins [32][33][34], ion solvation [35][36], small molecular clusters [37][38] and small molecules on surfaces [39][40][41]. While well-converged results

Association of aescin with β- and γ-cyclodextrins studied by DFT calculations and spectroscopic methods

• Ana I. Ramos,
• Pedro D. Vaz,
• Susana S. Braga and
• Artur M. S. Silva

Beilstein J. Nanotechnol. 2017, 8, 348–357, doi:10.3762/bjnano.8.37

• calculations by creating different complex geometries that could represent the real complex. The geometries were optimised at the M06-2X/6-31g(d) level with tight convergence criteria, including dispersion energy corrections (D3) and in the presence of a solvation model to simulate the presence of water. It

• should be mentioned that all atoms were optimised at the same level of theory, i.e., the ONIOM approach was not considered. Afterwards NMR chemical shifts were estimated at the more accurate M06-2X/6-311g(d,p) level with D3 correction and the solvation model, while using the GIAO algorithm. Furthermore

• evaluate the effects of solvation, to account for the effects of water the IEFPCM model was used for the description of the solvent continuum. Furthermore, the ONIOM approach was not used with all atoms being optimised at the same level of theory. The initial geometries of the hosts and the guest were

Single pyrimidine discrimination during voltage-driven translocation of osmylated oligodeoxynucleotides via the α-hemolysin nanopore

• Yun Ding and
• Anastassia Kanavarioti

Beilstein J. Nanotechnol. 2016, 7, 91–101, doi:10.3762/bjnano.7.11

• and the nucleobase. It is not clear whether or not those interactions are direct or indirect via the corresponding solvation shells. It is plausible that the presence of OsBp inside the constriction site provides a highly confined environment in which the modified nucleotide is forced to rearrange to

• a less favored configuration as well as to a different solvation shell that “carries along” only what is critically important; all these changes are then detected as current modulation and slower dwell time. In an attempt to understand the source of the differences between dT(OsBp) and dC(OsBp) we

A facile method for the preparation of bifunctional Mn:ZnS/ZnS/Fe₃O₄ magnetic and fluorescent nanocrystals

• Houcine Labiadh,
• Tahar Ben Chaabane,
• Romain Sibille,
• Lavinia Balan and
• Raphaël Schneider

Beilstein J. Nanotechnol. 2015, 6, 1743–1751, doi:10.3762/bjnano.6.178

• TEM because of the solvation layer around the QDs in aqueous solution. The lowest dH value of 11 nm was obtained for the Mn:ZnS/ZnS QDs. The dH increased with the thickness of the magnetic shell (Table 1). The highest dH (39 nm) was observed for Mn:ZnS/ZnS/Fe3O4 (3) nanocrystals. The DLS measurements

Multiscale modeling of lithium ion batteries: thermal aspects

• Arnulf Latz and
• Jochen Zausch

Beilstein J. Nanotechnol. 2015, 6, 987–1007, doi:10.3762/bjnano.6.102

• ) simulations once the force fields for the interaction between the molecules are known [14][15]. Information on interface properties can be obtained from MD simulations and from DFT simulations [15]. MD simulations are especially relevant to study the solvation properties of the ions [15][16][17], which are

• important to understand contribution of solvation forces to the intercalation kinetics. The actual barriers for intercalation can be addressed by DFT simulations [18]. The change in mechanical properties upon intercalation is very important to understand degradation phenomena in batteries. Usually the

• simulations the determination of Gibbs free energies, entropies and insertion properties (e.g., kinetic barriers, chemical potential of adsorbed species, solvation energies) are obtained. The relation of these quantities to the actual heat production has to be derived from systematic thermodynamic theories

Pulmonary surfactant augments cytotoxicity of silica nanoparticles: Studies on an in vitro air–blood barrier model

• Jennifer Y. Kasper,
• Lisa Feiden,
• Maria I. Hermanns,
• Christoph Bantz,
• Michael Maskos,
• Ronald E. Unger and
• C. James Kirkpatrick

Beilstein J. Nanotechnol. 2015, 6, 517–528, doi:10.3762/bjnano.6.54

• dispersing the freeze-dried surfactant mixture is not suitable to achieve solvation of the lipoproteins on the molecular level; even colloidally stabilized lipid/protein agglomerates are not reached. Furthermore, the study of the agglomeration behavior of silica nanoparticles in the presence of proteins is

Sequence-dependent electrical response of ssDNA-decorated carbon nanotube, field-effect transistors to dopamine

• Hari Krishna Salila Vijayalal Mohan,
• Jianing An and
• Lianxi Zheng

Beilstein J. Nanotechnol. 2014, 5, 2113–2121, doi:10.3762/bjnano.5.220

• phosphate groups. Consequently, the positively charged groups of DA are rendered free, thereby enabling them to interact with DNA bases. This allows DA to participate in the solvation mechanism of DNA bases through hydrogen bonding interactions. Thus, the group of DA is protonated during solvation by the

• by DA is determined by the strength and nature of the SWCNT–ssDNA and ssDNA–DA interactions [25][26]. The observed trend in the change of magnitude in transistor parameters could be addressed based on the contributions from the differences in the binding affinity, wrapping tendency and solvation

The surface properties of nanoparticles determine the agglomeration state and the size of the particles under physiological conditions

• Christoph Bantz,
• Olga Koshkina,
• Thomas Lang,
• Hans-Joachim Galla,
• C. James Kirkpatrick,
• Roland H. Stauber and
• Michael Maskos

Beilstein J. Nanotechnol. 2014, 5, 1774–1786, doi:10.3762/bjnano.5.188

• interactions, as described by the Flory–Huggins parameter, and solvent quality changes with salinity due to the solvation shell around ions. As a qualitative observation, the entanglements of the sample PEG@POS-NH2 dissolve at physiological ion strengths. In the presence of proteins, agglomerates can be

Magnesium batteries: Current state of the art, issues and future perspectives

• Rana Mohtadi and
• Fuminori Mizuno

Beilstein J. Nanotechnol. 2014, 5, 1291–1311, doi:10.3762/bjnano.5.143

Morphological characterization of fullerene–androsterone conjugates

• Alberto Ruiz,
• Margarita Suárez,
• Nazario Martin,
• Fernando Albericio and
• Hortensia Rodríguez

Beilstein J. Nanotechnol. 2014, 5, 374–379, doi:10.3762/bjnano.5.43

• dynamic light scattering (DLS) measures the hydrodynamic diameter of the particle including the solvation layers, while TEM gives the most direct information about the size distribution and shapes of the primary particles. DLS and TEM have different basis and can lead to discrepancies in sizing

Photoactivation of luminescence in CdS nanocrystals

• Valentyn Smyntyna,
• Bogdan Semenenko,
• Valentyna Skobeeva and
• Nikolay Malushin

Beilstein J. Nanotechnol. 2014, 5, 355–359, doi:10.3762/bjnano.5.40

• influence of humid argon and oxygen on the photoinduced amplification of the photoluminescence intensity of CdSe/ZnS quantum dots of is presented. It is suggested that this effect is the result of solvation of the charged states of the surface traps. Two competing processes may occur during the irradiation

Large-scale atomistic and quantum-mechanical simulations of a Nafion membrane: Morphology, proton solvation and charge transport

• Pavel V. Komarov,
• Pavel G. Khalatur and
• Alexei R. Khokhlov

Beilstein J. Nanotechnol. 2013, 4, 567–587, doi:10.3762/bjnano.4.65

• Department, Moscow State University, Moscow 119991, Russia 10.3762/bjnano.4.65 Abstract Atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in a hydrated Nafion membrane and the solvation and transport of protons in the water channel of the

• PEFCs [54][55][56][57][58][59]. There are excellent reviews that cover this subject in considerable detail [5][12][60]. In this paper, the atomistic and first-principles molecular dynamics simulations are employed to investigate the structure formation in hydrated Nafion membrane and the solvation and

• solvation shell for the ions (Figure 7). As the temperature is subsequently increased, the minimum for the contact ion pairs and solvent-separated ion pairs becomes deeper. More importantly, the main contribution to the free energy of contact ion pairs seems to be dominated by the entropy gain, not the

Nanoscopic surfactant behavior of the porin MspA in aqueous media

• Ayomi S. Perera,
• Hongwang Wang,
• Tej B. Shrestha,
• Deryl L. Troyer and
• Stefan H. Bossmann

Beilstein J. Nanotechnol. 2013, 4, 278–284, doi:10.3762/bjnano.4.30

• formation. Then the change in the chemical potential (Δμ°) during supramolecular aggregation is dependent on the transfer of MspA from the aqueous phase into the MspA-bilayer and the interaction of the head groups. The term (Δµº/kBT)transfer is negative, because the solvation of extended hydrophobic

• surfaces has a disruptive effect on the water structure. Whereas the hydrogen bond network of water around an alkane of modest length (e.g., C6H14) is not distorted significantly, the solvation of extended hydrophobic structures has a disruptive effect on the water structure because it prohibits the

Influence of the solvent on the stability of bis(terpyridine) structures on graphite

• Daniela Künzel and
• Axel Groß

Beilstein J. Nanotechnol. 2013, 4, 269–277, doi:10.3762/bjnano.4.29

• Daniela Kunzel Axel Gross Institute of Theoretical Chemistry, Ulm University, D-89069 Ulm, Germany 10.3762/bjnano.4.29 Abstract The effect of solvation on the adsorption of organic molecules on graphite at room temperature has been addressed with force-field molecular dynamics simulations. As a

• model system, the solvation of a bis(terpyridine) isomer in water and 1,2,4-trichlorobenzene was studied with an explicit solvation model. The inclusion of solvation has a noticeable effect on adsorption energies. Although the results of the various considered force fields differ quite significantly

• various network structures as a function of the chemical potential is derived yielding a sequence in agreement with the experiment. Keywords: computer simulations; energy related; force-field calculations; nanomaterials; solvation; Introduction The controlled formation of structured surfaces by the

Pulse-response measurement of frequency-resolved water dynamics on a hydrophilic surface using a Q-damped atomic force microscopy cantilever

• Masami Kageshima

Beilstein J. Nanotechnol. 2012, 3, 260–266, doi:10.3762/bjnano.3.29

• stiffness was determined and is attributed to the reported solidification of the hydration layers. Keywords: atomic force microscopy; hydration; pulse-response; quality-factor control; viscoelasticity; Introduction Liquid solvation is a phenomenon common to a large variety of liquid–solid interfaces [1

• ]. In particular, water solvation, or hydration, on hydrophilic surfaces has drawn interest because of its relevance to biological phenomena on the molecular scale. The dynamical properties of hydrated water have been reported to largely differ from those of bulk water based on the analysis of results

• . Utilizing the high spatial resolution of AFM, various intriguing properties of liquid solvation [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19], especially hydration [8][9][11][12][13][14][15][18][19], have been newly revealed. It should be noted that, in addition to its high spatial resolution, AFM

Towards a scalable and accurate quantum approach for describing vibrations of molecule–metal interfaces

• David M. Benoit,
• Bruno Madebene,
• Inga Ulusoy,
• Luis Mancera,
• Yohann Scribano and
• Sergey Chulkov

Beilstein J. Nanotechnol. 2011, 2, 427–447, doi:10.3762/bjnano.2.48

• for the interpretation of complex vibrational experiments. The first method offers a fully classical approach to anharmonic corrections that can easily include solvation (or more generally environment effects) and finite temperature effects. This latter aspect can be important in the case of