A quantum chemical treatment of solvation effects using the standard quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations is challenging due to QM and MM solvent exchange ...near the QM solute. To this end, various adaptive QM/MM methods have been proposed; free solvent exchanges are allowed via flexible switching of their identities between QM and MM systems depending on their distances from the QM solute. However, temporal and spatial discontinuities remain in the standard implementations of adaptive QM/MM approaches and continue to hamper stable and accurate dynamics simulations. We previously demonstrated that the size-consistent multipartitioning (SCMP) method achieves temporal continuity while, to some extent, avoiding spatial discontinuities. In the present study, we demonstrate that residual spatial discontinuities may lead to severe artifacts under certain conditions. Through quantitative analyses, we show that all multiscale including QM/MM methods might experience these problems, which so far have not been investigated in depth. To alleviate these artifacts, we propose a correction scheme in the framework of the SCMP approach and demonstrate its effectiveness using bulk water simulations.
In MtrF, an outer-membrane multiheme cytochrome, the 10 heme groups are arranged in heme binding domains II and IV along the pseudo-C₂ axis, forming the electron transfer (ET) pathways. Previous ...reports based on molecular dynamics simulations showed that the redox potential (E
m) values for the heme pairs located in symmetrical positions in domains II and IV were similar, forming bidirectional ET pathways Breuer M, Zarzycki P, Blumberger J, Rosso KM (2012) J Am Chem Soc 134(24):9868–9871. Here, we present the E
m values of the 10 hemes in MtrF, solving the linear Poisson–Boltzmann equation and considering the protonation states of all titratable residues and heme propionic groups. In contrast to previous studies, the E
m values indicated that the ET is more likely to be downhill from domain IV to II because of localization of acidic residues in domain IV. Reduction of hemes in MtrF lowered the E
m values, resulting in switching to alternative downhill ET pathways that extended to the flavin binding sites. These findings present an explanation of how MtrF serves as an electron donor to extracellular substrates.
For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) ...techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.
In order to establish effective conservation strategy, drivers of local and regional patterns of biodiversity need to be understood. The composition of local biodiversity is dependent on a number of ...factors including evolution and redistribution of lineages through dispersal and environmental heterogeneity. Brazilian canga is characterised by a ferrugineous substrate, found both in the Iron Quadrangle of Minas Gerais and in the Carajás mountains in Amazonia. Canga is one of several specialised habitat types comprising Brazilian campo rupestre, a montane vegetation found within or adjacent to several major Brazilian bioregions, including the Atlantic Forest and Amazonia, with exceptionally high levels of diversity and endemism arising from both history of dispersal and environmental variation. In order to inform biodiversity conservation for canga, and more broadly for campo rupestre, we performed floristic and phylogenetic analyses investigating affinities between 28 sites on different substrates (canga and quartzite) and geographic locations (Carajás, Pará Amazonia; Cadeia do Espinhaço, Minas Gerais; Chapada Diamantina, Bahia). Through analysis of 11204 occurrences of 4705 species of angiosperms, we found that Amazonian Carajás canga plant communities formed a cohesive group, distinct from species assemblages found in Eastern Brazil (Minas Gerais, Bahia), either on canga or quartzite. The phylogenetic megatree of species across all sites investigated shows associations between certain clades and Amazonian canga, with few shared species between the Amazonian Carajás and Eastern Brazil sites, while the floristic comparison shows high levels of heterogeneity between sites. The need for reserves for Amazonian Carajás canga has been recognized and addressed by the creation of a national park. However, current sampling does not provide sufficient reassurance that the canga areas now benefitting from full legal protection adequately represent the regional canga flora.
Abstract
A quantum chemistry study of the first singlet (
S
1
) and triplet (
T
1
) excited states of phenylsulfonyl-carbazole compounds, proposed as useful thermally activated delayed fluorescence ...(TADF) emitters for organic light emitting diode (OLED) applications, was performed with the quantum Equation-Of-Motion Variational Quantum Eigensolver (qEOM-VQE) and Variational Quantum Deflation (VQD) algorithms on quantum simulators and devices. These quantum simulations were performed with double zeta quality basis sets on an active space comprising the highest occupied and lowest unoccupied molecular orbitals (HOMO, LUMO) of the TADF molecules. The differences in energy separations between
S
1
and
T
1
(Δ
E
S
T
) predicted by calculations on quantum simulators were found to be in excellent agreement with experimental data. Differences of 17 and 88 mHa with respect to exact energies were found for excited states by using the qEOM-VQE and VQD algorithms, respectively, to perform simulations on quantum devices without error mitigation. By utilizing state tomography to purify the quantum states and correct energy values, the large errors found for unmitigated results could be improved to differences of, at most, 4 mHa with respect to exact values. Consequently, excellent agreement could be found between values of Δ
E
S
T
predicted by quantum simulations and those found in experiments.
We propose a new adaptive QM/MM method, the size-consistent multipartitioning (SCMP) QM/MM scheme, which enables stable and computationally efficient QM/MM simulations. A number of partitionings with ...identical size of the QM and the MM regions are considered with a new adaptive scheme in order to (1) realize smooth QM/MM switching, (2) introduce a conserved quantity (total energy, Hamiltonian), (3) avoid spurious artificial forces on the QM/MM border, and (4) allow for an efficient parallel implementation. Benchmark simulations performed for “QM water in MM water” show that energy conservation can be significantly improved and the computational efficiency allows treating also larger QM regions, for which previous methods had to face an intractable increase in computer time.
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