Search results for "Computation"

Modeling of biomolecular machines in non-equilibrium steady states

2021

Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate. Equilibrium statistical mechanics guides both the development of models and numerical methods for dynamics obeying detailed balance. For systems driven away from thermal equilibrium such a universal theoretical framework is missing. For a restricted class of driven systems governed by Markov dynamics and local detailed balance, stochastic thermodynamics has evolved to fill this gap and to provide fundamental constraints and guiding principles. The next step…

Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability

2021

Switching between different levels of resolution is essential for multiscale modeling, but restoring details at higher resolution remains challenging. In our previous study we have introduced deepBackmap: a deep neural-network-based approach to reverse-map equilibrated molecular structures for condensed-phase systems. Our method combines data-driven and physics-based aspects, leading to high-quality reconstructed structures. In this work, we expand the scope of our model and examine its chemical transferability. To this end, we train deepBackmap solely on homogeneous molecular liquids of small molecules, and apply it to a more challenging polymer melt. We augment the generator's objective w…

Book Review: Ion Solvation. By Y. Marcus

1987

Book Review: Ions in Solution: Basic Principles of Chemical Interactions. By J. Burgess

1989

Observable Electric Potential and Electrostatic Potential in Electrochemical Systems

1999

The role of the electric potential in the description of transport processes in electrochemical systems is critically analyzed. Since the electrostatic potential drop between two parts of a system ...

Molecular precursors of mesostructured silica materials in the atrane route: A DFT/GIAO/NBO theoretical study

2007

Abstract Quantum chemical calculations using density functional theory have been carried out to investigate two assumed molecular precursors and identified as silatranes (N[OCH2CH2]3Si–OCH2CH2N–(CH2CH2OH)2 and N[OCH2CH2]3Si–OCH2CH2N–(CH2CH2OH)2Na+) which are present in the synthesis of mesoporous silica based material namely “the atrane route”. One of the ways in this synthesis leads to the well-known MCM-41. Additionally, in this work has been also investigated two others molecules such as triethanolamine (TEAH3) and sodatrane which are present in the medium. Gas phase and solution equilibrium geometries of the previous molecules were fully optimized at B3LYP level, modeling solvent effect…

DFT calculation of structures and NMR chemical shifts of simple models of small diameter zigzag single wall carbon nanotubes (SWCNTs)

2011

Linearly conjugated benzene rings (acenes), belt-shape molecules (cyclic acenes) and model single wall carbon nanotubes (SWCNTs) were fully optimized at the unrestricted level of density functional theory (UB3LYP/6-31G*). The models of SWCNTs were selected to get some insight into the potential changes of NMR chemical shift upon systematic increase of the molecular size. The theoretical NMR chemical shifts were calculated at the B3LYP/pcS-2 level of theory using benzene as reference. In addition, the change of radial breathing mode (RBM), empirically correlated with SWCNT diameter, was directly related with the radius of cyclic acenes. Both geometrical and NMR parameters were extrapolated t…

Identity Double-Proton Transfer in (3Z)-3-Hydroxy-1,4-di(quinolin-2-yl)but-3-en-2-one

2003

Although there is a very fast (on the NMR timescale) double-proton transfer in (1Z,3Z)-3-hydroxy-4-quinolin-2-yl-1-quinolin-2(1H)-ylidenbut-3-en-2-one (the product of the condensation of ethyl oxalate with 2-lithiomethylquinoline), it is the only species present in chloroform solution. Comparison of the product of condensation of ethyl oxalate with 2-lithiomethyl derivatives of pyridine (recent studies) and quinoline (present studies) shows that benzoannulation considerably affects the tautomeric equilibrium. The observed changes are not only quantitative but also qualitative. Moreover, contrary to the proton transfer in the pyridine tautomers, this process is fast in the quinoline tautomer…

Comparative NMR and IR spectral, X-ray structural and theoretical studies of eight 6-arylidenedibenzo[b,e]thiepin-11-one-5,5-dioxides

2007

Abstract Eight 6-arylidenedibenzo[b,e]thiepin-11-one-5,5-dioxides are characterized by NMR and IR spectroscopy. Single crystal X-ray structures for three congeners are reported. In addition, the transmission of substituent effects in conjugated double bond system of 6-arylidenedibenzo[b,e]thiepin-11-one-5,5-dioxide framework has been evaluated by calculating the correlations between selected 13C NMR chemical shifts and IR stretching wave numbers and Hammett constants of the substituents locating in the phenyl ring of the arylidene moiety.

Electronic Structures and Spectroscopic Properties of 6π-Electron Ring Molecules and Ions E2N2 and E42+ (E = S, Se, Te)

2004

The electronic structures and molecular properties of square-planar 6π-electron ring molecules and ions E2N2 and E42+ (E = S, Se, Te) were studied using various ab initio methods and density functionals. All species were found to contain singlet diradical character in their electronic structures. Detailed analysis of the CAS wave function of S2N2 in terms of different valence bond structures gives the largest weight for a Lewis-type singlet diradical VB structure in which the two unpaired electrons reside on nitrogen atoms, though the relative importance of the different VB structures is highly dependent on the level of theory. The diradical character in both E2N2 and E42+ was found to incr…