Full Ab Initio Methods Research Articles

Combining Quantum Mechanics and Machine-Learning Calculations for Anharmonic Corrections to Vibrational Frequencies.

Several methods are available to compute the anharmonicity in semirigid molecules. However, such methods are not yet routinely employed because of their high computational cost, especially for large molecules. The potential energy surface is required and generally approximated by a quartic force field potential based on ab initio calculation, thus limiting this approach to medium-sized molecules. We developed a new, fast, and accurate hybrid quantum mechanics/machine learning (QM/ML) approach to reduce the computational time for large systems. With this novel approach, we evaluated anharmonic frequencies of 37 molecules, thus covering a broad range of vibrational modes and chemical environments. The obtained fundamental frequencies reproduce results obtained using B2PLYP/def2tzvpp with a root-mean-square deviation (RMSD) of 21 cm-1 and experimental results with a RMSD of 23 cm-1. Along with this very good accuracy, the computational time with our hybrid QM/ML approach scales linearly with N, while the traditional full ab initio method scales as N2, where N is the number of atoms.

Ab initio study of the electron energy loss function in a graphene-sapphire-graphene composite system

The propagator of a dynamically screened Coulomb interaction W in a sandwichlike structure consisting of two graphene layers separated by a slab of Al2O3 (or vacuum) is derived from single-layer graphene response functions and by using a local dielectric function for the bulk Al2O3. The response function of graphene is obtained using two approaches within the random phase approximation (RPA): an ab initio method that includes all electronic bands in graphene and a computationally less demanding method based on the massless Dirac fermion (MDF) approximation for the low-energy excitations of electrons in the π bands. The propagator W is used to derive an expression for the effective dielectric function of our sandwich structure, which is relevant for the reflection electron energy loss spectroscopy of its surface. Focusing on the range of frequencies from THz to mid-infrared, special attention is paid to finding an accurate optical limit in the ab initio method, where the response function is expressed in terms of a frequency-dependent conductivity of graphene. It was shown that the optical limit suffices for describing hybridization between the Dirac plasmons in graphene layers and the Fuchs-Kliewer phonons in both surfaces of the Al2O3 slab, and that the spectra obtained from both the ab initio method and the MDF approximation in the optical limit agree perfectly well for wave numbers up to about 0.1 nm−1. Going beyond the optical limit, the agreement between the full ab initio method and the MDF approximation was found to extend to wave numbers up to about 0.3 nm−1 for doped graphene layers with the Fermi energy of 0.2 eV.

First-Principles Study of the Ultrafast, Laser-Induced Spin Transferability in the Multi-center Magnetic Cluster Ni3Na2

Using a full ab initio method, based on quantum chemical wave function methods with the inclusion of spin-orbit coupling and a static external magnetic field, we investigate the laser-induced, ultrafast spin transfer in the three-magnetic-center cluster Ni3Na2 under various static distortions. In this manuscript we study and identify three important factors, i.e. the interatomic distances, the number of bridging atoms, and the spin direction, in order to obtain a series of rules of thumb. It is found that the spin transfer between Ni atoms mainly depends on the number of Na atoms and the spin direction on the Ni atoms, and only the scenarios between Ni2 and Ni3 atoms with the spin direction at Ni3 atom along the x and z axes can be achieved.

Unified theory of ultrafast femtosecond and conventional picosecond magnetic dynamics in the distorted three-center magnetic cluster Ni3Na2

With the use of a full ab initio method, based on quantum chemical wave function methods with the inclusion of spin-orbit coupling and a static external magnetic field, we investigate the laser-induced ultrafast magnetic switching in the three-magnetic-center cluster Ni${}_{3}$Na${}_{2}$ under various static distortions. Thus we (i) establish spin dynamics as an unprecedentedly accurate sensor of the bond length between metallic centers, and (ii) derive a unified picture of ultrafast (femtosecond) and slow (ps, phonon-magnon) spin dynamics in molecular magnets by combining electron-spin and electron-lattice coupling. The resulting unexpectedly rich set of magnetic phases is exploited in order to provide time scales of phonon-magnon mediated spin dynamics in magnetic molecules.

Location of Si Vacancies and [Ti(OSi)4] and [Ti(OSi)3OH] Sites in the MFI Framework: A Large Cluster and Full Ab Initio Study

Titanium silicalite-1 (TS-1) is an important catalyst for selective oxidation reactions. However, the nature and structure of the active sites and the mechanistic details of the catalytic reactions over TS-1 have not been well-understood, leaving a continuous debate on the genesis of active sites on the TS-1 surface in the literature. In this work, the location of Si vacancies and [Ti(OSi)(4)] and [Ti(OSi)(3)OH] sites in the MFI (Framework Type Code of ZSM-5 (Zeolite Socony Mobile-Five)) framework has been studied using a full ab initio method with 40T clusters with a Si:Ti molar ratio of 39:1. It was shown that the former four energetically favorable sites for Si vacancies are T6, T12, T4, and T8 and for Ti centers of [Ti(OSi)(4)] are T10, T4, T8 and T11, being partially the same sites. Whether by replacing Si vacancies or substituting the fully coordinated Si sites, the most preferential site for Ti is T10, which indicates that the insertion mechanism does not affect the favorable sites of Ti in the MFI lattice. For the defective [Ti(OSi)(3)OH] sites, it was found that the Si vacancy at T6 with a Ti at its neighboring T9 site (T6-def-T9-Ti pair) is the most energetically favorable one, followed by a T6-def-T5-Ti pair with a small energy gap. These findings are significant to elucidate the nature of the active sites and the mechanism of reactions catalyzed by TS-1 and to design the TS-1 catalyst.

On the Lifetime of Suspended Atomic Chains Formed from Stretched Metallic Gold Nanowires

number of atoms as a function of tem- perature. We have carried out classical molecular dynamics simulations using tight-binding models with a second moment approximations. Our results suggest a more complex phenomenon than pre- viously anticipated. The dynamics of chain rupture seems to be determined beyond thermodynamics contributions and the bond breaking patterns were observed to be chain-length dependent. these systems; continuous, mixed models with empiri- cal potentials, and even ab initio ones. In this work we have theoretically investigated the lifetime of suspended atomic chains (LACs) formed from stretched gold NWs. Experimental LAC formation involves stochastic aspects which implies the need of considering many cases at dif- ferent conditions (temperature, pulling velocities, crys- tallographic orientations, etc.). The large number of cases and size of the structures (hundreds of atoms) pre- cludes the use of full ab initio methods due to the high computational cost. A natural choice to study these sys- tems could be to use embedded atom potential (EAM) (31, 32) or tight-binding model with second moment ap- proximations (TB-SMA) (33, 34). EAM and TB-SMA have good records of well describing metallic structures. Our choice was to use TB-SMA by the reasons detailed in the methodology section.

Computational Studies on Polymer Adhesion at the Surface of γ-Al2O3. I. The Adsorption of Adhesive Component Molecules from the Gas Phase

We calculate the minimum energy paths and reaction energies of the adsorption of the epoxide adhesive components diglycidylesterbisphenol A (DGEBA), diethyltriamine (DETA), and the adhesion promoter 3-aminopropylmethoxysilane (AMEO) at two different sites on a model of the native Al2O3 surface, using the nudged elastic band algorithm in conjunction with self-consistent charge-density functional based tight binding. Our results show that the chosen combination of methods is well suited to obtain an overview of the reaction mechanisms and kinetics of the adsorption of organic molecules on inorganic surfaces. The obtained MEP-s show that there is preference for the adsorption of the adhesion promoter, AMEO, over the resin, DGEBA, while the adsorption of the curing agent, DETA, is unfavorable. Our approach also gives an insight into the ranges of the mechanical and electronic influences of the adsorption process on the interface, which neither full ab initio methods nor force field approaches can provide. These results will help to develop a quantum mechanics-molecular mechanics multiscale embedding scheme for more detailed studies of organic/inorganic hybrid interface reactions.

The embedded ion method: A new approach to the electrostatic description of crystal lattice effects in chemical shielding calculations

AbstractThe nuclear magnetic shielding anisotropy of NMR active nuclei is highly sensitive to the nuclear electronic environment. Hence, measurements of the nuclear magnetic shielding anisotropy represent a powerful tool in the elucidation of molecular structure for a wide variety of materials. Quantum mechanical ab initio nuclear magnetic shielding calculations effectively complement the experimental NMR data by revealing additional structural information. The accuracy and capacity of these calculations has been improved considerably in recent years. However, the inherent problem of the limitation in the size of the systems that may be studied due to the relatively demanding computational requirements largely remains. Accordingly, ab initio shielding calculations have been performed predominantly on isolated molecules, neglecting the molecular environment. This approach is sufficient for neutral nonpolar systems, but leads to serious errors in the shielding calculations on polar and ionic systems. Conducting ab initio shielding calculations on clusters of molecules (i.e., including the nearest neighbor interactions) has improved the accuracy of the calculations in many cases. Other methods of simulating crystal lattice effects in shielding calculations that have been developed include the electrostatic representation of the crystal lattice using point charge arrays, full ab initio methods, ab initio methods under periodic boundary conditions, and hybrid ab initio/molecular dynamics methods. The embedded ion method (EIM) discussed here follows the electrostatic approach. The method mimics the intermolecular and interionic interactions experienced by a subject molecule or cluster in a given crystal in quantum mechanical shielding calculations with a large finite, periodic, and self‐consistent array of point charges. The point charge arrays in the EIM are generated using the Ewald summation method and embed the molecule or ion of interest for which the ab initio shielding calculations are performed. The accuracy with which the EIM reproduces experimental nuclear magnetic shift tensor principal values, the sensitivity of the EIM to the parameters defining the point charge arrays, as well as the strengths and limitations of the EIM in comparison with other methods that include crystal lattice effects in chemical shielding calculations, are presented. © 2006 Wiley Periodicals, Inc. Concepts Magn Reson Part A 28A: 347–368, 2006

Theoretical study of vitamin properties from combined QM-MM methods: Comparison of chemical shifts and energy

The combination of quantum mechanics (QM) and molecular mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM-MM method has been used for different types of problems, for example, structural biology, surface phenomena, and the liquid phase. In this paper, we have implemented these methods for vitamins, an important kind of biological molecule, and then compared results. The calculations were done by the full ab initio method (HF/3–21 g and HF/6–31 g) and QM-MM (ONIOM) method with HF(3–21 g)/AM1/UFF; then, we found that the geometry obtained by the QM-MM method is very accurate and this rapid method can be used in place of time consuming ab initio methods for large molecules. A comparison of energy values in the QM-MM and QM methods is given. We compare chemical shifts and conclude that the QM-MM method is a perturbed full QM method.

QM/MM model study on properties and structure of some antibiotics in gas phase: Comparison of energy and NMR chemical shift

The combination of Quantum Mechanics (QM) and Molecular Mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM/MM method has been used for different types of problems, for example: structural biology, surface phenomena, and liquid phase. In this paper, we have used these methods for antibiotics and then we compare results. The calculations were done by the full ab initio method (HF/3-21G) and the (HF/STO-3G) and QM/MM (ONIOM) method with HF (3-21G)/AM1/UFF and HF (STO-3G)/AM1/UFF. We found the geometry that has obtained by the QM/MM method to be very accurate, and we can use this rapid method in place of time consuming ab initio methods for large molecules. Comparison of energy values in the QM/MM and QM methods is given. In the present work, we compare chemical shifts and conclude that the QM/MM method is a perturbed full QM method. The work has been done on penicillin, streptomycin, benzyl penicillin, neomycin, kanamycin, gentamicin, and amoxicillin.

Multilayer Formulation of the Fragment Molecular Orbital Method (FMO)

The fragment molecular orbital method (FMO) has been generalized to allow for multilayer structure. Fragments are assigned to layers, and each layer can be described with a different basis set and/or level of electron correlation. Interlayer boundaries are treated in the general spirit of the FMO method since they also coincide with some interfragment boundaries. The question of the one- and two-layer FMO accuracy dependence upon the fragmentation scheme is also addressed. The new method has been applied to predict the reaction barrier and the reaction heat for the Diels-Alder reaction with a representative set of reactants based on dividing fragments in two layers. The 6-31G* basis set has been used for the active site and the 6-31G*, 6-31G, 3-21G, and STO-3G basis sets have been used for the substituents. Different levels of electron correlation (RHF, B3LYP, and MP2) have been applied to layers in systematic fashion. The one-layer FMO errors in the reaction barrier and the reaction heat were 2.0 kcal/mol or less for all levels applied (RHF, B3LYP, and MP2), relative to full ab initio methods. For the two-layer method the error was found to be several kcal/mol. Benchmark calculations of the activation barrier for the decarboxylation of phenylcyanoacetate by beta-cyclodextrin demonstrated that the two-layer calculations are efficient, being 36 times faster than the regular DFT, as well as accurate, with the error being 1.0 kcal/mol.

Comparison of Fundamental and Harmonic Frequencies of First-Row Closed-Shell Diatomics Calculated Using Full ab Initio Methods and Composite Methods

The fundamental frequencies of vibration of 12 first-row closed-shell diatomics have been predicted using both full and composite levels of CCSD(T) ab initio theory. For a given CPU time budget, composite levels of theory were found to predict harmonic frequencies significantly better than full ab initio methods. However, little improvement was obtained in the computation of the anharmonic correction with composite methods, its being already well predicted at the CCSD(T) small basis set level. It was found that for a given CPU time budget the most accurate fundamental frequencies are obtained by performing a calculation of the harmonic frequencies using a composite method where the optimal choice of basis sets involved a larger cc-pVXZ basis set only 1 greater in the valence designation compared with the smaller basis set. An anharmonic correction computed using a small basis set or a low-level composite method could then be added to these harmonic frequencies. The implication of these findings is that ac...

A comparative study on the structure of M2Se and M2I+ (M = Ag, Au) using pseudopotentials and full Ab initio methods

AbstractThe molecules of M2Se and M2I+ (M = Ag, Au) are used as test models to study the quality of the pseudopotential methodology when using the Hartree–Fock and second‐order Møller‐Plesset methods. We have used two implementations of the Wadt and Hay pseudopotentials: the new large‐ and small‐core pseudopotentials (known as LANL 1DZ and LANL2DZ in GAUSSIAN‐92) and the traditional one used for a long time. It is found that the optimum geometry depends on the type of pseudopotential selected. A comparison with the results computed when all the electrons are taken explicitly into account shows that the new LANL1DZ and LANL2DZ give the right answer. Using these potentials, the geometry and potential energy surface of the M2Se and M2I+ systems is explored and its optimum geometry found. © 1994 John Wiley & Sons, Inc.