Charges derived from electrostatic potentials: Exploring dependence on theory and geometry optimization levels for dipole moments

Conformation- and phosphorylation-dependent electron tunnelling across self-assembled monolayers of tau peptides

We report on charge transport across self-assembled monolayers (SAMs) of short tau peptides by probing the electron tunneling rates and quantum mechanical simulation. We measured the electron tunneling rates across SAMs of carboxyl-terminated linker molecules (C₆H₁₂O₂S) and short cis-tau (CT) and trans-tau (TT) peptides, supported on template-stripped gold (Au^TS) bottom electrode, with Eutectic Gallium-Indium (EGaIn)(EGaIn) top electrode. Measurements of the current density across thousands of Au^TS/linker/tau//Ga₂O₃/EGaIn single-molecule junctions show that the tunneling current across CT peptide is one order of magnitude lower than that of TT peptide. Quantum mechanical simulation demonstrated a wider energy bandgap of the CT peptide, as compared to the TT peptide, which causes a reduction in its electron tunneling current. Our findings also revealed the critical role of phosphorylation in altering the charge transport characteristics of short peptides; more specifically, we found that the presence of phosphate groups can reduce the energy band gap in tau peptides and alter their electrical properties. Our results suggest that conformational and phosphorylation of short peptides (e.g., tau) can significantly change their charge transport characteristics and energy levels.

Polarization Switching Method for Effective Free Energy Calculation of Membrane Translocation on the Nano-scale

Free-energy calculations are crucial for investigating biomolecular interactions on the Nano-scale level. However, in theoretical studies, the neglect of electronic polarization can jeopardize their accuracy and correct predictive capabilities, specifically...

Effects of electrostatic drag on the velocity of hydrogen migration - pre- and post-transition state enthalpy/entropy compensation

Ab initio molecular dynamics calculations were used to explore the underlying factors that modulate the velocity of hydrogen migration for 1,2 hydrogen shifts in carbocations in which different groups interact noncovalently with the migrating hydrogen. Our results indicate that stronger electrostatic interactions between the migrating hydrogen and nearby π-systems lead to slower hydrogen migration, an effect tied to entropic contributions from the hydrogen + neighboring group substructures.

Highly efficient CO2 capture and conversion of a microporous acylamide functionalized rht-type metal–organic framework

A microporous acylamide functionalized rht-type MOF (HNUST-9) with Lewis acidic open copper sites and CO₂-philic acylamide groups exhibits high performance for CO₂ capture, separation and chemical conversion.

Computational prediction of promising pyrazine and bipyridine analogues of a fluorinated MOF platform, MFN-Ni-L (M = SI/AL; N = SIX/FIVE; L = pyr/bipyr), for CO2 capture under pre-humidified conditions

The CO2 separation performance has been explored under dry and pre-humidified conditions for the fluorinated metal organic frameworks SIFSIX-Ni-pyr, ALFFIVE-Ni-pyr, SIFSIX-Ni-bipyr and ALFFIVE-Ni-bipyr, which are incorporated with/without a coordinatively unsaturated site (CUS), Al, and organic linkers 1,4-pyrazine and 4,4'-bipyridine. The ultra-small pore size (∼4 Å) of the pyrazine analogues of fluorinated-MOFs, i.e. SIFSIX-Ni-pyr and ALFFIVE-Ni-pyr, showed infinite selectivity towards CO2 with low uptake capability under dry conditions, which drastically reduced to 0 wt% under very low pre-humidification conditions (∼10-15 wt% adsorbed moisture). In marked contrast, the bipyridine analogues SIFSIX-Ni-bipyr and ALFFIVE-Ni-bipyr showed significant CO2 capture performance of up to 30-40 wt% with pre-humidification. Further, both SIFSIX-Ni-bipyr and ALFFIVE-Ni-bipyr showed high CO2 selectivity as well as good working capacity at 1-10 bar while poor selectivity is observed for the pyrazine analogues with pre-humidification. The incorporation of Al as a CUS provides stability to the ALFFIVE-Ni-bipyr fluorinated-MOF under pre-humidified conditions due to the ability of Al to co-ordinate with water molecules in hydrogen bonded networks. Therefore, to develop physisorption-based CO2 capturing processes under pre-humidified conditions, the use of Al incorporated ALFFIVE-Ni-bipyr is highly suitable, which may outperform most of the fluorinated-MOFs and other classes of porous solids reported so far.

Theoretical study of an anti-Markovnikov addition reaction catalyzed by β-cyclodextrin

β-Cyclodextrin (β-CD) has a hydrophilic exterior and a hydrophobic internal cavity, which allows it to form host-guest complexes with a wide range of guests, such as organics, inorganics, and biomolecules. The aforementioned features lead to an extensive range of applications of β-CD, as the properties of β-CD mean that it is environmentally friendly and can be recovered and reused without mass loss. Here, the β-CD-catalyzed anti-Markovnikov addition of styrene to thiophenol in the presence of aerial oxygen and in aqueous solution to give 1-phenyl-2-(phenylsulfanyl)-1-ethanol was studied using density functional theory (DFT) and the Hartree-Fock (HF) method. The optimal configuration of the inclusion complex of styrene and thiophenol within β-CD was obtained, which indicated that styrene and thiophenol enter from the secondary and primary hydroxyl ends of β-CD, respectively. Moreover, hydrogen bonding of β-CD with styrene and thiophenol contributes to the stability of the inclusion complex. An investigation of the charges from electrostatic potentials using a grid-based method (CHELPG) highlighted the distribution of atomic charges upon complexation. The reaction sites of styrene and thiophenol were determined based on electrostatic potentials (ESPs) and condensed dual descriptors. The calculated ¹H nuclear magnetic resonance (¹H NMR) spectrum of β-CD implied that the chemical shifts of its protons change and H3 and H5 move to higher fields upon complexation, while the calculated ¹³C nuclear magnetic resonance (¹³C NMR) spectrum of styrene suggested that this molecule is electrophilic. Graphical abstract ᅟ.

Dynamic/Thermochemical Balance Drives Unusual Alkyl/F Exchange Reactions in Siloxides and Analogs

A recent report has shown that siloxides can undergo an unusual Me/F exchange reaction promoted by NF3 in the gas phase ( Angew. Chem. Int. Ed. 2012, 51, 8632-8635). A more extensive study of this kind of exchange has been carried out using mass spectrometry techniques (FT-ICR), DFT calculations, natural bond orbital (NBO) analysis, and Born-Oppenheimer molecular dynamics simulations (BOMD), using NF3, SO2F2, and CF4 as fluorine donors and evaluating the effect of replacing the Si center by Ge and C. This comprehensive approach shows that NF3 is crucial for the exchange reaction, as SO2F2 forms SO3F(-) via a pentacoordinated channel whereas no reaction is observed for CF4. The uniqueness of NF3 is caused by favorable thermochemical consideration and by dynamic effects that preclude the formation of the ubiquitous Si-F pentacoordinated species. Me3GeO(-) was shown to be as reactive as siloxides toward NF3, whereas C analogs showed no reactions under our experimental conditions. The exchange reaction was also shown to take place for triethylsiloxides. These exchange reactions are examples of reaction systems that avoid the lower energy pathway and are driven by dynamic effects that cannot be explained by the potential energy surface.

Molecular properties of the PCO radical: heat of formation and the isomerization pathways

The potential energy surface of [P,C,O] system in the ground state was investigated by quantum chemical methods. Four different isomers were characterized at the B3LYP/aug-cc-pVTZ: COP (i1), cPCO (i2), PCO (i3), and CPO (i4). The linear species i3 is the global minimum in the ground state surface, while i4 is a bent structure, and i2 is a cyclic isomer. In view to evaluate the bond nature of each isomer, a QTAIM and a NBO analyses were applied. The triangular species presents a ring critical point which confirms its cyclic structure instead of a T-shape one. The stability increases in the following order: i3 > i2 > i1 > i4. The energy gap between i3 and i2 ranges from 49.20 to 51.15 kcal mol(-1). The reaction barrier energies that converge into the direction of i3 showed values around 10 kcal mol(-1), while the reverse barriers are considerably large (62.85 kcal mol(-1)). The i3 heat of formation at 298 K ranges from 11.83 to 19.41 kcal mol(-1).

A new generation of B(n)N(n) rings as a supplement to boron nitride tubes and cages

In B(n)N(n) cages or tubes, when the quasi-borazine rings are attached to each other through a pair of common atoms of B and N, the bonding structure is named class A. On the other hand, there are some B(n)N(n) rings including a covalent bond between two atoms of B and N, which are named class B. In all previous studies, both reports of synthesis and theoretical calculation of boron nitride tubes and cages, the quasi-borazine units are attached together like class A. There are no theoretical or experimental reports from class B compounds except for a brief study in our previous works (Struct. Chem. 2012, 23, 551-580; J. Phys. Chem. C 2010, 114, 15315.). In this study, we have used two kinds of boron nitride rings from a twisted BN sheet in the same chirality created by different mechanisms. For (4, 4) chirality, the molecules B(16)N(16) and B(15)N(15) are found to respectively represent class A and B, and for (5, 5) chirality the molecules B(20)N(20) and B(18)N(18) are respectively again of class A and B. The structure of class A rings is similar to boron nitride tubes, but we have shown that it is impossible to produce a macromolecule of class B form as tubes or cages, because there is much more instability and intermolecular tension in macro forms of class B. This is the main reason that the class B molecules are rare and, because of their small size, have not yet been synthesized, although we have some suggestions for the synthesis of these kinds of molecules. The stability and electromagnetic properties with hybrid density functional theory using the EPR-III and EPR-II basis sets for explanation of hyperfine parameters and spin densities, electrical potential, and isotropic Fermi coupling constant of these rings have been studied by the nonbonded interaction models. Normal mode analyses including aromaticity have been investigated by using the nucleus independent chemical shift values at the ring center. Interaction energy and gain in energy aid in describing the stability that is promoted upon gradual binding with molecular hydrogen, and a linear relationship occurred between them.

PHEMTO: protein pH-dependent electric moment tools

PHEMTO (protein pH-dependent electric moment tools) is released in response to the high demand in protein science community for evaluation of electrostatic characteristics in relations to molecular recognition. PHEMTO will serve protein scientists with new advanced features for analysis of protein molecular interactions: Electric/dipole moments, their pH-dependence and in silico charge mutagenesis effects on these properties as well as alternative algorithms for electric/dipole moment computation--Singular value decomposition of electrostatic potential (EP) to account for reaction field. The implementation is based on long-term experience--PHEI mean field electrostatics and PHEPS server for evaluation of global and local pH-dependent properties. However, PHEMTO is not just an update of our PHEPS server. Besides standard electrostatics, we offer new, advanced and useful features for analysis of protein molecular interactions. In addition our algorithms are very fast. Special emphasis is given to the interface--intuitive and user-friendly. The input is comprised of the atomic coordinate file in Protein Data Bank format. The advanced user is provided with a special input section for addition of non-polypeptide charges. The output covers actually full electrostatic characteristics but special emphasis is given to electric/dipole moments and their interactive visualization. PHEMTO server can be accessed at http://phemto.orgchm.bas.bg/.

Molecular simulation of carbon dioxide/methane/hydrogen mixture adsorption in metal-organic frameworks

This work performs a systematic computational study toward a molecular understanding of the separation characteristics of metal-organic frameworks (MOFs), for which the purification of synthetic gas by two representative MOFs, MOF-5 and Cu-BTC, is adopted as an example. The simulations show that both geometry and pore size affect largely the separation efficiency, complex selectivity behaviors with different steps can occur in MOFs, and the electrostatic interactions that exist can enhance greatly the separation efficiency of gas mixtures composed of components with different chemistries. Furthermore, the macroscopic separation behaviors of the MOF materials are elucidated at a molecular level to give insight into the underlying mechanisms. The findings as well as the molecular-level elucidations provide useful microscopic information toward a complete understanding of the separation characteristics of MOFs that may lead to general design strategies for synthesizing new MOFs with tailored properties, as well as guiding their practical applications.