562 research outputs found
A unified electrostatic and cavitation model for first-principles molecular dynamics in solution
No full textThe electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon
Influence of growth and preparation condition on the reconstruction of SiC(001) surfaces: a first principles study
No full text
Water confined in nanotubes and between graphene sheets: a first principle study
No full textWater confined at the nanoscale has been the focus of numerous experimental and theoretical investigations in recent years, yet there is no consensus on such basic properties as diffusion and the nature of hydrogen bonding (HB) under confinement. Unraveling these properties is important to understand fluid flow and transport at the nanoscale, and to shed light on the solvation of biomolecules. Here we report on a first principle, computational study focusing on water confined between prototypical nonpolar substrates, i.e., single-wall carbon nanotubes and graphene sheets, 1-2.5 nm apart. The results of our molecular dynamics simulations show the presence of a thin, interfacial liquid layer (∼5 Å) whose microscopic structure and thickness are independent of the distance between confining layers. The properties of the HB network are very similar to those of the bulk outside the interfacial region, even in the case of strong confinement. Our findings indicate that the perturbation induced by the presence of confining media is extremely local in liquid water, and we propose that many of the effects attributed to novel phases under confinement are determined by subtle electronic structure rearrangements occurring at the interface with the confining medium
A unified electrostatic and cavitation model for first-principles molecular dynamics in solution
No full textThe electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon. (c) 2006 American Institute of Physics.THEO
A unified electrostatic and cavitation model for first-principles molecular dynamics in solution
No full textThe electrostatic continuum solvent model developed by Fattebert and Gygi is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. The model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution, and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. They apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon
Combining amine metabolomics and quantitative proteomics of cancer cells using derivatization with isobaric tags
No full textQuantitative metabolomics and proteomics technologies are powerful approaches to explore cellular metabolic regulation. Unfortunately, combining the two technologies typically requires different LC-MS setups for sensitive measurement of metabolites and peptides. One approach to enhance the analysis of certain classes of metabolites is by derivatization with various types of tags to increase ionization and chromatographic efficiency. We demonstrate here that derivatization of amine metabolites with tandem mass tags (TMT), typically used in multiplexed peptide quantitation, facilitates amino acid analysis by standard nanoflow reversed-phase LC-MS setups used for proteomics. We demonstrate that this approach offers the potential to perform experiments at the MS1-level using duplex tags or at the MS2-level using novel 10-plex reporter ion-containing isobaric tags for multiplexed amine metabolite analysis. We also demonstrate absolute quantitative measurements of amino acids conducted in parallel with multiplexed quantitative proteomics, using similar LC-MS setups to explore cellular amino acid regulation. We further show that the approach can also be used to determine intracellular metabolic labeling of amino acids from glucose carbons
PHD3 loss in cancer enables metabolic reliance on fatty acid oxidation via deactivation of ACC2
No full textWhile much research has examined the use of glucose and glutamine by tumor cells, many cancers instead prefer to metabolize fats. Despite the pervasiveness of this phenotype, knowledge of pathways that drive fatty acid oxidation (FAO) in cancer is limited. Prolyl hydroxylase domain proteins hydroxylate substrate proline residues and have been linked to fuel switching. Here, we reveal that PHD3 rapidly triggers repression of FAO in response to nutrient abundance via hydroxylation of acetyl-coA carboxylase 2 (ACC2). We find that PHD3 expression is strongly decreased in subsets of cancer including acute myeloid leukemia (AML) and is linked to a reliance on fat catabolism regardless of external nutrient cues. Overexpressing PHD3 limits FAO via regulation of ACC2 and consequently impedes leukemia cell proliferation. Thus, loss of PHD3 enables greater utilization of fatty acids but may also serve as a metabolic and therapeutic liability by indicating cancer cell susceptibility to FAO inhibition
Accuracy of a Recent Regularized Nuclear Potential
No full textF. Gygi recently
suggested an analytic, norm-conserving, regularized
nuclear potential to enable all-electron plane-wave calculations [Gygi J. Chem. Theory Comput. 2023, 19, 1300–1309.]. This potential V(r) is determined by inverting the Schrödinger equation
for the wave function Ansatz ϕ(r) = exp[−h(r)]/√π with h(r) = r erf(ar) + b exp(−a2r2), where a and b are
parameters. Gygi fixes b by demanding ϕ to
be normalized, with the value b(a) depending on the strength of the regularization controlled by a. We begin this work by re-examining the determination
of b(a) and find that the original
10-decimal tabulations of Gygi are only correct to 5 decimals, leading
to normalization errors in the order of 10–10. In
contrast, we show that a simple 100-point radial quadrature scheme
not only ensures at least 10 correct decimals of b but also leads to machine-precision level satisfaction of the normalization
condition. Moreover, we extend Gygi’s plane-wave study by examining
the accuracy of V(r) with high-precision
finite element calculations with Hartree–Fock and LDA, GGA,
and meta-GGA functionals on first- to fifth-period atoms. We find
that although the convergence of the total energy appears slow in
the regularization parameter a, orbital energies
and shapes are indeed reproduced accurately by the regularized potential
even with relatively small values of a, as compared
to results obtained with a point nucleus. The accuracy of the potential
is furthermore studied with s-d excitation
energies of Sc–Cu as well as ionization potentials of He–Kr,
which are found to converge to sub-meV precision with a = 4. The findings of this work are in full support of Gygi’s
contribution, indicating that all-electron plane-wave calculations
can be accurately performed with the regularized nuclear potential
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