Learn More
Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in(More)
The proper understanding of biomolecular recognition mechanisms that take place in a drug target is of paramount importance to improve the efficiency of drug discovery and development. The intrinsic dynamic character of proteins has a strong influence on biomolecular recognition mechanisms and models such as conformational selection have been widely used to(More)
o-Nitrobenzaldehyde is photolabile because of an irreversible phototautomerization, whereas comparable aromatic compounds function as photoprotectors because the tautomerization is reversible. In this experimental and theoretical study we track down the cause of this difference to the electronic changes that occur during the tautomerization.
With the rise in antibiotic resistance, there is interest in discovering new drugs active against new targets. Here, we investigate the dynamic structures of three isoprenoid synthases from Mycobacterium tuberculosis using molecular dynamics (MD) methods with a view to discovering new drug leads. Two of the enzymes, cis-farnesyl diphosphate synthase(More)
Aromaticity is a central chemical concept widely used in modern chemistry for the interpretation of molecular structure, stability, reactivity, and magnetic properties of many compounds. As such, its reliable prediction is an important task of computational chemistry. In recent years, many methods to quantify aromaticity based on different physicochemical(More)
Ab initio surface-hopping dynamics calculations have been performed to simulate the intramolecular excited state hydrogen transfer dynamics of ortho-nitrobenzaldehyde (o-NBA) in the gas phase from the electronic S(1) excited state. Upon UV excitation, the hydrogen is transferred from the aldehyde substituent to the nitro group, generating o-nitrosobenzoic(More)
The experimental UV/vis absorption spectrum of ortho-nitrobenzaldehyde (o-NBA) has been assigned by means of MS-CASPT2/CASSCF, TD-DFT, and RI-CC2 theoretical computations. Additional information on the nature of the absorbing bands was obtained by comparing the o-NBA spectrum with that of related compounds, as, e.g., nitrobenzene and benzaldehyde. For(More)
The lack of reference aromatic systems in the realm of inorganic aromatic compounds makes the evaluation of aromaticity in all-metal and semimetal clusters a difficult task. To date, calculation of nucleus-independent chemical shifts (NICS) has been the most widely used method to discuss aromaticity in these systems. In the first part of this work, we(More)
As compared to classical organic aromatic compounds, the evaluation of aromaticity in all-metal and semimetal clusters is much more complex. For a series of these clusters, it is frequently found that different methods used to discuss aromaticity lead to divergent conclusions. For this reason, there is a need to evaluate the reliability of the different(More)
The effect of three in-plane (bond length alternation, bond length elongation, and clamping) and three out-of-plane deformations (boatlike, chairlike, and pyramidalization) on the aromaticity of the benzene molecule has been analyzed employing seven widely used indicators of aromaticity. It is shown that only the aromatic fluctuation index (FLU) is able to(More)