# year-2001

Publications during 2001

- 15 years of Car-Parrinello simulations in physics, chemistry and biology
- A review with 348 refs. In 1985, Car and Parrinello published a seminal article on an "Unified approach for mol. dynamics and d. functional theory". This paper established a basis for parameter-free mol. dynamics simulations in which all the interactions are calcd. on the fly via a first-principles quantum mech. method. In the 15 yr of its existence, the Car-Parrinello method has found widespread applications that expanded rapidly from physics to chem. and, most recently, even into biol. In this article, the foundations of the method in its most common implementation, the one based on d. functional theory, plane wave basis sets and pseudopotentials are described and extensions to the original scheme are outlined. The current power of Car-Parrinello simulations is illustrated by presenting selected case studies and possible future directions are sketched in the final outlook. [on SciFinder (R)]
- A First Principles Exploration of a Variety of Active Surfaces and Catalytic Sites in Ziegler−Natta Heterogeneous Catalysis
- We present a Car−Parrinello investigation of various active surfaces and catalytic sites in a realistic Ziegler−Natta heterogeneous system. We examine the (100), (110), and (104) surfaces of the MgCl2 support and the related binding of the possible mononuclear and dinuclear catalyst configurations. Relaxation and/or reconstruction processes affect these surfaces in varying degrees, according to the different Miller indexes. We find that TiCl4 and Ti2Cl6 species can bind as stable adducts, depending on the morphology of the surface considered. However, the activation and polymerization phases show that destabilization phenomena can affect the dinuclear species during the catalysis reaction. This provides a new insight into the ability of the different centers to give rise to the real polymerization process. Finally, we present a first attempt to address the role of a typical donor phthalate at a fully first principles level.
- A First-Principles Computation of the Low-Energy Polymorphic Forms of the Acetic Acid Crystal. A Test of the Atom−Atom Force Field Predictions
- A New ab-Initio Approach for NMR Chemical Shifts in Periodic Systems
- We present a new method for computing NMR chemical shifts and magnetic susceptibilities in extended systems through an ab initio density functional perturbation theory approach. The method is applicable to crystalline and amorphous insulators under periodic boundary conditions, as well as to isolated molecules. The formalism exploits the exponentially decaying nature of localized Wannier orbitals. We have implemented the method in the context of a plane wave pseudopotential approach. The results are in good agreement with experiment and with calculations that use other theoretical methods.
- A new constant-pressure ab initio/classical molecular dynamics method: simulation of pressure-induced amorphization in a Si35H36 cluster
- A novel implicit Newton–Raphson geometry optimization method for density functional theory calculations
- Ab initio molecular dynamics simulation of the Ag(111)-water interface
- Ab initio molecular dynamics simulation of the Cu(110)–water interface
- Ab initio molecular dynamics study of the pressure-induced phase transformations in cristobalite
- The mechanism for the pressure-induced transformation of cristobalite to stishovite and post-stishovite phases has been obtained from constant pressure ab initio molecular dynamics simulations. The cristobalite to stishovite transformation is found to be a two step process where SiO4 tetrahedra first rotate followed by a lattice distortion to yield the six-coordinated stishovite structure. Further compression of stishovite yields the CaCl2 structure and is followed by another six-coordinated structure with symmetry P21/n (at 11 Mbars) which remains stable to a pressure of about 14 Mbars and then transforms into a nine-coordinated P21/m structure.
- Ab Initio Molecular Dynamics-Based Assignment of the Protonation State of Pepstatin A/HIV-1 Protease Cleavage Site
- A recent 13C NMR experiment (Smith et al. Nature Struct. Biol. 1996, 3, 946−950) on the Asp 25-Asp25‘ dyad in pepstatin A/HIV-1 protease measured two separate resonance lines, which were interpreted as being a singly protonated dyad. We address this issue by performing ab initio molecular dynamics calculations on models for this site accompanied by calculations of 13C NMR chemical shifts and isotopic shifts. We find that already on the picosecond time-scale the model proposed by Smith et al. is not stable and evolves toward a different monoprotonated form whose NMR pattern differs from the experimental one. We suggest, instead, a different protonation state in which both aspartic groups are protonated. Despite the symmetric protonation state, the calculated 13C NMR properties are in good agreement with the experiment. We rationalize this result using a simple valence bond model, which explains the chemical inequality of the two C sites. The model calculations, together with our calculations on the complex, allow also the rationalization of 13C NMR properties on other HIV-1 PR/inhibitor complexes. Both putative binding of the substrate to the free enzyme, which has the dyad singly protonated (Piana, S.; Carloni, P. Proteins: Struct., Funct., Genet. 2000, 39, 26−36), and pepstatin A binding to the diprotonated form are consistent with the inverse solvent isotope effect on the onset of inhibition of pepsin by pepstatin and the kinetic iso-mechanism proposed for aspartic proteases (Cho, T.-K.; Rebholz, K.; Northrop, D.B. Biochemistry 1994, 33, 9637−9642).
- Ab initio simulation of charged slabs at constant chemical potential
- Accurate Total Energies without Self-Consistency
- We present a new way of calculating approximate but accurate total energies within the framework of density functional theory. Our technique is based on an expansion of the energy functional to second order and does not require self-consistent iterations of the total density. The functional can be minimized by using the same techniques as developed for variational density functional perturbation theory. The method is ideally suited to systems composed of weakly interacting fragments, but it can also be applied to semiconductors and insulators. We show the versatility of our approach in a variety of examples exhibiting different types of chemical bonding.
- Action-Derived Molecular Dynamics in the Study of Rare Events
- We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural application in the study of rare events. Its capabilities are illustrated by nontrivial examples. The algorithm lends itself to straightforward parallelization, and when combined with ab initio molecular dynamics it promises to offer a powerful tool for the study of chemical reactions.
- An anomalous alloy: YxSi1-x
- The structural and dynamical properties of the rare earth silicon amorphous alloy YxSi1-x for x=0.093 and 0.156 are studied via density functional-based molecular dynamics. The Si network forms cavities in which a Y3+ cation is entrapped. Its electrons are transferred to the Si network and are located in the dangling bonds of the Si atoms that line the Y cavities. This leads to the presence of low coordinated Si atoms that can be described as monovalent or divalent anions. For x=0.156, the cavities touch each other and share Si atoms that have two dangling bonds. The vibrational spectrum is similar to that of amorphous Si. However, yttrium doping induces a shoulder at 70 cm-1 and a pronounced peak at 180 cm-1 due to low coordinated Si.
- Autoionization in Liquid Water
- Car-parrinello molecular dynamics investigation of active surfaces and Ti catalytic sites in Ziegler-Natta heterogeneous catalysis
- Car–Parrinello molecular dynamics of the SN2 reaction Cl−+Cl2CH2
- Classical molecular dynamics simulations of amorphous silica surfaces
- We have adapted classical molecular dynamics to study the structural and dynamical properties of amorphous silica surfaces. Concerning the structure, the density profile exhibits oscillations perpendicularly to the surface as observed in liquid metal surfaces and the pair correlation functions as well as the angle distributions show features (absent in the interior of the films) that can be attributed to the presence of twofold rings which are perpendicular to the surface. From the mean-squared displacement of the non-bridging oxygen atoms we find that in the interior region they move perpendicular to the surface while they move parallel to it in the surface region.
- Dehydroxylation and Silanization of the Surfaces of β-Cristobalite Silica: An ab Initio Simulation
- Dehydroxylation and silanization processes on the silica surface are studied by ab initio molecular dynamics. The (100) and (111) surfaces of β-cristobalite are used as two possible models of the hydroxylated amorphous surface. The activation energy and latent heat for the dehydroxylation reactions of the (100) surface computed by constrained ab initio molecular dynamics are in reasonable agreement with experimental data on the amorphous surface. Adhesion reactions of silanes are simulated aiming at elucidating the binding mechanism of organosilanes used for instance as silica−polymer coupling agents. The simulation have provided insights on the occurrence of multiple silica−silane bonds and on the role of hydrolization of silane by physisorbed water in the adhesion on the wet surface.
- Density functional calculations for polymers and clusters - progress and limitations