Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method

Nakata, Hisao; Fedorov, Dmitri G.; Zahariev, Federico; Schmidt, Michael W.; Kitaura, Kazuo; Gordon, Mark S.; Nakamura, Shinichiro

doi:10.1063/1.4915068

Cited by 12 publications

(4 citation statements)

References 95 publications

(114 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For comparison, IR and Raman spectra without fragmentation are provided in the Supporting Information (Figure S1). Consistent with previous similar comparisons for the ground state, ,− FMO reproduces spectra quite well. The heights of a few peaks show some deviations, more for Raman than for IR, attributed to the use of third derivatives in Raman activities, which are more sensitive to fragmentation.…”

Section: Resultssupporting

confidence: 91%

Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method

Nakata

Fedorov

2023

J. Chem. Theory Comput.

View full text Add to dashboard Cite

The analytic energy gradient of energy with respect to nuclear coordinates is derived for the fragment molecular orbital (FMO) method combined with time-dependent density functional theory (TDDFT). The response terms arising from the use of a polarizable embedding are derived. The obtained analytic FMO-TDDFT gradient is shown to be accurate in comparison to both numerical FMO-TDDFT and unfragmented TDDFT gradients, at the level of two- and three-body expansions. The gradients are used for geometry optimizations, molecular dynamics, vibrational calculations, and simulations of IR and Raman spectra of excited states. The developed method is used to optimize the geometry of the ground and excited electronic states of the photoactive yellow protein (PDB: 2PHY).

show abstract

Section: Resultssupporting

confidence: 91%

Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method

Nakata

Fedorov

2023

J. Chem. Theory Comput.

View full text Add to dashboard Cite

show abstract

“…Based on this chemical intuition, the total electronic energy of the system could be obtained by a proper combination of the divided subsystems . In recent years, many fragmentation methods have been developed, such as the fragment molecular orbital (FMO), − the molecular fractionation with conjugate caps (MFCC) approach, ,− the molecular tailoring approach (MTA), ,, the systematic fragmentation method (SFM), ,− the generalized many-body fragmentation (GEBF) , method, the kernel energy method (KEM), − the combined fragmentation method (CFM), ,,, the electrostatically embedded many-body expansion (EE-MB), , the explicit polarization (X-pol) potential, , the many-overlapping-body (MOB) expansion, and the generalized many-body expansion (GMBE). − …”

Section: Introductionmentioning

confidence: 99%

Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method

Jin

Zhang

2017

J. Phys. Chem. A

View full text Add to dashboard Cite

In this study, the electrostatically embedded generalized molecular fractionation with conjugate caps (concaps) method (EE-GMFCC) was employed for efficient linear-scaling quantum mechanical (QM) calculation of total energies of RNAs. In the EE-GMFCC approach, the total energy of RNA is calculated by taking a proper combination of the QM energy of each nucleotide-centric fragment with large caps or small caps (termed EE-GMFCC-LC and EE-GMFCC-SC, respectively) deducted by the energies of concaps. The two-body QM interaction energy between non-neighboring ribonucleotides which are spatially in close contact are also taken into account for the energy calculation. Numerical studies were carried out to calculate the total energies of a number of RNAs using the EE-GMFCC-LC and EE-GMFCC-SC methods at levels of the Hartree-Fock (HF) method, density functional theory (DFT), and second-order many-body perturbation theory (MP2), respectively. The results show that the efficiency of the EE-GMFCC-SC method is about 3 times faster than the EE-GMFCC-LC method with minimal accuracy sacrifice. The EE-GMFCC-SC method is also applied for relative energy calculations of 20 different conformers of two RNA systems using HF and DFT, respectively. Both single-point and relative energy calculations demonstrate that the EE-GMFCC method has deviations from the full system results of only a few kcal/mol.

show abstract

“…The higher-order derivative has analytical advantages because small features such as shoulders in the spectrum appear as maxima and minima, measuring the wavelength or energy position of the features more accurately, and it derives better qualitative information. Usually, in spectroscopy, the second derivative is used to calculate harmonic frequencies and associated properties, such as the vibrational contribution to the free energy, infrared (IR) intensities, Raman activities, and the zero-point energy [47]. In our case, the double derivative of the real part of the DF shows three minima at 1.43 eV, 2.16 eV, and 3.58 eV in figure 10 To verify the experimental optical absorption and dielectric properties of the materials we have used DFT to calculate the DF and density of states.…”

Section: Resultsmentioning

confidence: 99%

Cathodoluminescence and optical absorption spectroscopy of plasmonic modes in chromium micro-rods

Ghorai¹,

Ghosh²,

Das³

et al. 2022

Nanotechnology

View full text Add to dashboard Cite

Manipulating light at the sub-wavelength level is a crucial feature of surface plasmon resonance (SPR) properties for a wide range of nanostructures. Noble metals like Au and Ag are most commonly used as SPR materials. Significant attention is being devoted to identify and develop non-noble metal plasmonic materials, whose optical properties can be reconfigured for plasmonic response by structural phase changes. Chromium(Cr) which supports plasmon resonance, is a transition metal with shiny finished, highly non-corrosive, and bio-compatible alloys, making it an alternative plasmonic material. We have synthesized Cr micro-rods from a bi-layer of Cr/Au thin films, which evolves from Face Centered Cubic (FCC) to Hexagonal Close Packed (HCP) phase by thermal activation in a forming gas ambient. We employed optical absorption spectroscopy and cathodoluminescence (CL) imaging spectroscopy to observe the plasmonic modes from the Cr micro-rod. The origin of three emission bands that spread over UV-Vis-IR wavelength is established theoretically by considering the critical points of the second-order derivative of the macroscopic dielectric function obtained from density functional theory (DFT) matches with interband/intraband transition of electrons observed in density of states vs. energy graph. The experimentally observed CL emission peaks closely match the s-d and d-d band transition obtained from DFT calculations. Our findings on plasmonic modes in Cr(HCP) phase can expand the range of plasmonic material beyond noble metal with tunable plasmonic emissions for plasmonic-based optical technology.

show abstract

Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method

Cited by 12 publications

References 95 publications

Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method

Analytic Gradient for Time-Dependent Density Functional Theory Combined with the Fragment Molecular Orbital Method

Full QM Calculation of RNA Energy Using Electrostatically Embedded Generalized Molecular Fractionation with Conjugate Caps Method

Cathodoluminescence and optical absorption spectroscopy of plasmonic modes in chromium micro-rods

Contact Info

Product

Resources

About