A New Interpretation of the Structure and Solvent Dependence of the Far UV Circular Dichroism Spectrum of Short Oligopeptides

2019 ◽  
Author(s):  
Anshuman Kumar ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Cd Spectra ◽  
Functional Theory ◽  
Polyproline Ii ◽  
Solvent Dependence ◽  
Explicit Consideration ◽  
New Interpretation ◽  
Implicit And Explicit ◽  
Explicit Water

In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory’s isolated pair hypothesis.

A New Interpretation of the Structure and Solvent Dependence of the Far UV Circular Dichroism Spectrum of Short Oligopeptides

2019 ◽  
Author(s):  
Anshuman Kumar ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Cd Spectra ◽  
Functional Theory ◽  
Polyproline Ii ◽  
Solvent Dependence ◽  
Explicit Consideration ◽  
New Interpretation ◽  
Implicit And Explicit ◽  
Explicit Water

In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory’s isolated pair hypothesis.

Quasicontinuum-Like Reduction of Density Functional Theory Calculations of Nanostructures

2008 ◽  
Vol 8 (7) ◽  
pp. 3729-3740
Author(s):  
Dan Negrut ◽  
Mihai Anitescu ◽  
Anter El-Azab ◽  
Peter Zapol
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Cost ◽  
Density Functional Theory Calculations ◽  
Optimization Techniques ◽  
Electronic Density ◽  
Functional Theory ◽  
Cross Domain ◽  
Explicit Consideration ◽  
Orbital Free

Density functional theory can accurately predict chemical and mechanical properties of nanostructures, although at a high computational cost. A quasicontinuum-like framework is proposed to substantially increase the size of the nanostructures accessible to simulation. It takes advantage of the near periodicity of the atomic positions in some regions of nanocrystalline materials to establish an interpolation scheme for the electronic density in the system. The electronic problem embeds interpolation and coupled cross-domain optimization techniques through a process called electronic reconstruction. For the optimization of nuclei positions, computational gains result from explicit consideration of a reduced number of representative nuclei and interpolating the positions of the rest of nuclei following the quasicontinuum paradigm. Numerical tests using the Thomas-Fermi-Dirac functional demonstrate the validity of the proposed framework within the orbital-free density functional theory.

On the Linear Geometry of Lanthanide Hydroxide (Ln—OH, Ln=La-Lu)

2019 ◽  
Author(s):  
Hassan Harb ◽  
Lee Thompson ◽  
Hrant Hratchian
Keyword(s):  
Triple Bond ◽  
Density Functional ◽  
Valence Electron ◽  
Density Functional Theory Calculations ◽  
Electron Configuration ◽  
Functional Theory ◽  
Key Species ◽  
Pi Orbitals ◽  
Lanthanide Hydroxide ◽  
Linear Geometry

Lanthanide hydroxides are key species in a variety of catalytic processes and in the preparation of corresponding oxides. This work explores the fundamental structure and bonding of the simplest lanthanide hydroxide, LnOH (Ln=La-Lu), using density functional theory calculations. Interestingly, the calculations predict that all structures of this series will be linear. Furthermore, these results indicate a valence electron configuration featuring an occupied sigma orbital and two occupied pi orbitals for all LnOH compounds, suggesting that the lanthanide-hydroxide bond is best characterized as a covalent triple bond.

On the Linear Geometry of Lanthanide Hydroxide (Ln—OH, Ln=La-Lu)

2019 ◽  
Author(s):  
Hassan Harb ◽  
Lee Thompson ◽  
Hrant Hratchian
Keyword(s):  
Triple Bond ◽  
Density Functional ◽  
Valence Electron ◽  
Density Functional Theory Calculations ◽  
Electron Configuration ◽  
Functional Theory ◽  
Key Species ◽  
Pi Orbitals ◽  
Lanthanide Hydroxide ◽  
Linear Geometry

Lanthanide hydroxides are key species in a variety of catalytic processes and in the preparation of corresponding oxides. This work explores the fundamental structure and bonding of the simplest lanthanide hydroxide, LnOH (Ln=La-Lu), using density functional theory calculations. Interestingly, the calculations predict that all structures of this series will be linear. Furthermore, these results indicate a valence electron configuration featuring an occupied sigma orbital and two occupied pi orbitals for all LnOH compounds, suggesting that the lanthanide-hydroxide bond is best characterized as a covalent triple bond.

Is a Non-Transition Element Nitride Ferromagnet Ever Achievable? Indication of the N-N Pairing Instability

2006 ◽  
Vol 71 (11-12) ◽  
pp. 1525-1531 ◽  
Author(s):  
Wojciech Grochala
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Transition Element ◽  
Density Functional Theory Calculations ◽  
Functional Theory

The enthalpy of four polymorphs of CaN has been scrutinized at 0 and 100 GPa using density functional theory calculations. It is shown that structures of diamagnetic calcium diazenide (Ca2N2) are preferred over the cubic ferromagnetic polymorph (CaN) postulated before, both at 0 and 100 GPa.

scholarly journals Chalcogen Bond versus Weak Hydrogen Bond: Changing Contributions in Determining the Crystal Packing of [1,2,5]-Chalcogenadiazole-Fused Tetracyanonaphthoquinodimethanes

2021 ◽  
Vol 03 (02) ◽  
pp. 090-096
Author(s):  
Yusuke Ishigaki ◽  
Kota Asai ◽  
Takuya Shimajiri ◽  
Tomoyuki Akutagawa ◽  
Takanori Fukushima ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Density Functional ◽  
Molecular Design ◽  
Crystal Packing ◽  
Cyano Group ◽  
Density Functional Theory Calculations ◽  
Weak Hydrogen Bond ◽  
Functional Theory ◽  
Chalcogen Bond ◽  
Thiadiazole Ring

The crystal structures of a series of tetracyanonaphthoquinodimethanes fused with a selenadiazole or thiadiazole ring revealed that their molecular packing is determined mainly by two intermolecular interactions: chalcogen bond (ChB) and weak hydrogen bond (WHB). ChB between Se and a cyano group dictates the packing of selenadiazole derivatives, whereas the S-based ChB is much weaker and competes with WHB in thiadiazole analogues. This difference can be explained by different electrostatic potentials as revealed by density functional theory calculations. A proper molecular design that weakens WHB can change the contribution of ChB in determining the crystal packing of thiadiazole derivatives.

scholarly journals Tensor-structured algorithm for reduced-order scaling large-scale Kohn–Sham density functional theory calculations

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Chih-Chuen Lin ◽  
Phani Motamarri ◽  
Vikram Gavini
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Large Scale ◽  
Density Functional Theory Calculations ◽  
System Size ◽  
Real Space ◽  
Functional Theory ◽  
Reduced Order ◽  
Separable Approximation ◽  
Tensor Basis

AbstractWe present a tensor-structured algorithm for efficient large-scale density functional theory (DFT) calculations by constructing a Tucker tensor basis that is adapted to the Kohn–Sham Hamiltonian and localized in real-space. The proposed approach uses an additive separable approximation to the Kohn–Sham Hamiltonian and an L1 localization technique to generate the 1-D localized functions that constitute the Tucker tensor basis. Numerical results show that the resulting Tucker tensor basis exhibits exponential convergence in the ground-state energy with increasing Tucker rank. Further, the proposed tensor-structured algorithm demonstrated sub-quadratic scaling with system-size for both systems with and without a gap, and involving many thousands of atoms. This reduced-order scaling has also resulted in the proposed approach outperforming plane-wave DFT implementation for systems beyond 2000 electrons.

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