Car-Parrinello molecular dynamics on massively parallel computers.
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Journal Article↗
Biomedical subjects
Alessandro Curioni
Publications and source records attributed to Alessandro Curioni.
Disproving a silicon analog of an alkyne with the aid of topological analyses of the electronic structure and ab initio molecular dynamics calculations.
A silicon compound has recently been synthesized that was claimed to exhibit the first realization of a silicon-silicon triple bond. We debate this classification on the basis of a thorough investigation of the nature of the chemical bond, using the rigorous topological analysis of the electron density as developed in Bader's atoms-in-molecules theory, that of the electron localization function and the related orbital-independent definitions of the bond order. Our results refer both to the ground-state geometry and to nonequilibrium configurations, which are accessed by the system in a room-temperature ab initio molecular dynamics simulation. We also use the reciprocal compliance force constant as an independent chemical descriptor. All the above procedures are in agreement and do not support the classification of the silicon-silicon central bond as triple. The characterization which consistently emerges from the present study is one in which two electron pairs participate in the bonding and the other pair belongs mainly to nonbonding regions.
Alkynes↗
Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields.
A methodology aimed at improving the accuracy of current docking-scoring procedures is proposed, and validated through detailed tests of its performance in predicting the activity of HIV-1 protease inhibitors. This methodology is based on molecular dynamics simulations using a force field whose effective charges are refined by means of a novel procedure that relies on quantum-mechanical calculations and preserves the internal consistency of the parameterization scheme.
Drug Design↗
Broken inter-C60 bonds as the cause of magnetism in polymeric C60: a density functional study using C60 dimers.
Bond breaking in C60-C60 dimeric units is believed to play an important role in the onset of magnetism in 2D polymeric C60. On the basis of density-functional theory, the calculations we present here provide further insight into this mechanism through a quantitative characterization of the bond-breaking processes in the isolated dumbbell-shaped C60 dimer. In particular, the analysis of the calculated potential energy surfaces for the low-lying singlet and triplet states identifies and locates the S0-T2 crossing point, which is crucial for the transition to a magnetic state to take place under thermal conditions. These results also suggest a possible new approach to the production of magnetic polymeric C60.
Letter↗
Ab initio design of high-k dielectrics: La(x)Y1-xAlO3.
We use calculations based on density-functional theory in the virtual crystal approximation for the design of high-k dielectrics, which could offer an alternative to silicon dioxide in complementary metal-oxide semiconductor devices. We show that aluminates LaxY1-xAlO3 alloys derived by mixing aluminum oxide with lanthanum and yttrium oxides have unique physical attributes for a possible application as gate dielectrics when stabilized in the rhombohedral perovskite structure, and which are lost in the orthorhombic modification. Stability arguments locate this interesting composition range as 0.2<x<0.4. Phase separation in microdomains is shown to have the tendency to further enhance the dielectric constant. We propose this as a novel family of high-k dielectrics deserving experimental exploration.
Journal Article↗
Calculation of nonadiabatic couplings in density-functional theory.
This paper proposes methods for calculating the derivative couplings between adiabatic states in density-functional theory (DFT) and compares them with each other and with multiconfigurational self-consistent field calculations. They are shown to be accurate and, as expected, the costs of their calculation scale more favorably with system size than post-Hartree-Fock calculations. The proposed methods are based on single-particle excitations and the associated Slater transition-state densities to overcome the problem of the unavailability of multielectron states in DFT which precludes a straightforward calculation of the matrix elements of the nuclear gradient operator. An iterative scheme employing linear-response theory was found to offer the best trade-off between accuracy and efficiency. The algorithms presented here have been implemented for doublet-doublet excitations within a plane-wave-basis and pseudopotential framework but are easily generalizable to other excitations and basis sets. Owing to their fundamental importance in cases where the Born-Oppenheimer separation of motions is not valid, these derivative couplings can facilitate, for example, the treatment of nonadiabatic charge transfers, of electron-phonon couplings, and of radiationless electronic transitions in DFT.
Journal Article↗
Effects of nitridation on the characteristics of silicon dioxide: dielectric and structural properties from ab initio calculations.
By combining ab initio calculations and classical molecular dynamics, we determine how the inclusion of nitrogen in a silica matrix changes its dielectric constant, and elucidate the underlying mechanisms. We find that there is an entire range of nitrogen concentrations (up to approximately 25%) for which the structural pattern of the oxide is preserved in bulk SiON, and the dielectric constant increases mainly because of the variation of the ionic polarizability. This behavior is not sensitive to hydrogen passivation of nitrogen. The few defects, which are associated with electron states near the gap, are mainly centered on undercoordinated nitrogen and undercoordinated silicon, and tend to be removed by hydrogen.
Journal Article↗
The elusiveness of coffee aroma: new insights from a non-empirical approach.
Aroma is central to a pleasurable eating/drinking experience but is one of the most labile components of food. Coffee is an outstanding example. Attempts to avoid or control aroma degradation are often frustrated by ignorance of the microscopic mechanisms that are responsible for it. One of the processes most frequently invoked is radical formation, yet the identity of the radicals and their involvement in aroma degradation are poorly understood at the molecular level. Here a step forward in the fundamental understanding of this complex problem is taken by identifying the most relevant radicals and their products using first-principles calculations. Over 100 radicals originating from key aroma compounds found in coffee and other foods have been studied and classified according to an unambiguous criterion: their thermodynamic stability relative to common radical sources. This classification scheme predicts that most aroma molecules are resistant to both peroxidation and attack from phenolic antioxidants but are unstable with respect to radicals such as .OH. Dimers--generated from radical reactions--were also considered, and the most volatile species, which may further contribute to coffee aroma degradation, were focused on. Those--which are very few indeed--that have this potential have been identified.
Coffee↗
The binding mode of progesterone to its receptor deduced from molecular dynamics simulations.
An unambiguous understanding of the binding mode of human progesterone to its receptor still eludes experimental search. According to the X-ray structure of the ligand-binding domain, only one (O3) of the two keto groups at the ligand ends (O3 and O20) should play a role. This result is in conflict with chemical intuition and the results of site-directed mutagenesis experiments. Herein, we report classical molecular dynamics simulations that reveal the dynamic nature of the binding in solution, elucidate the reasons why X-ray studies failed to determine the role of O20, and clarify the effects of the mutations. The predictive power of the force field is ensured by the consistent introduction of a first-principles representation of the ligand.
Binding Sites↗
Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations.
Divalent metal ions are essential to many enzymatic reactions involving nucleic acids, but their critical and specific role still needs to be uncovered. Restriction endonucleases are a prominent group of such metal-requiring enzymes. Large scale accurate simulations of Mg- and Ca-BamHI elucidate the mechanism of the catalytic reaction leading to DNA cleavage and show that it involves the concerted action of two metal ions and water molecules. It is also established that what is decisive for the dramatically different behavior of magnesium (a cocatalyst) and calcium (an inhibitor) are kinetic factors and not the properties of the prereactive states of the enzymes. A new perspective is opened for the understanding of the functional role of metal ions in biological processes.
Calcium↗
Studies in the assessment of folding quality for protein modeling and structure prediction.
A diagnostic for assessing the quality of a fold has been developed to which further criteria can be progressively added. The goal is to create a measure that can follow the status of a protein structure in a simulation or modeling process, when the answer (the experimental structure) is not known in advance, rather than simply reject deliberate misfolds. This places greater emphasis on the need to study, and calibrate against, marginal cases, i.e., unusual native structures, incomplete structures, partially erroneous X-ray structures, good models, poor models, and the effect of cofactors. The first three terms introduced in the diagnostic are appropriate core-forming properties or noncore properties of residues in relation to tertiary structure, appropriate neighboring structure density for each residue in relation to tertiary structure, and secondary structure consistency. While the method emerges as a useful simulation analysis tool, we find a need for further fine-tuning to diminish sensitivity to minor conformational changes that retain essential features of the fold, balanced against the need to obtain a more sensitive response when a conformational change involves less physically meaningful interatomic interactions. This dual utility is difficult to obtain: the investigation highlights some of the issues. Initial attempts to obtain it have led to terms in the diagnostic that are admittedly complex: simplifications must also be explored.
Animals↗