A Hartree–Fock, MP2 and DFT computational study of the structures and energies of ″b2 ions derived from deprotonated peptides. A comparison of method and basis set used on relative product stabilities

2004 ◽  
Vol 675 (1-3) ◽  
pp. 149-162 ◽  
Author(s):  
Gregory A. Chass ◽  
Christopher N.J. Marai ◽  
David H. Setiadi ◽  
Imre G. Csizmadia ◽  
Alex G. Harrison
Keyword(s):  
Computational Study ◽  
Basis Set ◽  
Hartree Fock ◽  
Relative Product ◽  
Deprotonated Peptides

scholarly journals A computational study of Trishomocubane amino acid dipeptide

2004 ◽  
Author(s):  
◽  
Poomani Penny Govender
Keyword(s):  
Amino Acid ◽  
Computational Study ◽  
Building Blocks ◽  
Conformational Space ◽  
Basis Set ◽  
Peptide Design ◽  
Helical Structures ◽  
Hartree Fock ◽  
C Terminus ◽  
Acetyl Group

4-amino-(D3)-trishomocubane-4-carboxylic acid (tris-amino acid) is a constrained a-amino acid residue that exhibits peculiar conformational characteristics. The aim of the present study is to provide a deeper understanding of these features, which can be used as a guide when chOOSing@shomocubane as suitable building blocks for peptide design. The Ca carbon of@ishomocubane forms part of the cyclic structure, and consequently a peptidic environment was simulated with an acetyl group on its N-terminus and a methyl amide group on its C-terminus. This study involved a complete exploration of the conformational profile of (Yishomocubane using computational techniques.The parm94 parametization of the AMBER oio forc@eld was used to explore the conformational space of the peptide,Q)\xEFshomocubane. The Ramachandran maps computed at the molecular mechanics level' with the parm94 forc@\xEFeld parameters compared reasonably with the corresponding maps computed at the Hartree Fock (HF) level, using the 6-31G* basis set. The results of this study revealed that the conformational profile of the @ishomocubane peptide can be characterized by four low energy regions, viz., C7ax, C7eq, 310 and al helical structures.

A Comprehensive Computational Study on OCH+-Rg (Rg = He, Ne, Ar, Kr, Xe) Complexes

2003 ◽  
Vol 68 (3) ◽  
pp. 489-508 ◽  
Author(s):  
Yinghong Sheng ◽  
Jerzy Leszczynski
Keyword(s):  
Computational Study ◽  
Relativistic Effects ◽  
Dft Method ◽  
Basis Set ◽  
Rare Gas ◽  
Geometrical Parameters ◽  
Minor Effect ◽  
Dissociation Energies ◽  
Equilibrium Geometries

The equilibrium geometries, harmonic vibrational frenquencies, and the dissociation energies of the OCH+-Rg (Rg = He, Ne, Ar, Kr, and Xe) complexes were calculated at the DFT, MP2, MP4, CCSD, and CCSD(T) levels of theory. In the lighter OCH+-Rg (Rg = He, Ne, Ar) rare gas complexes, the DFT and MP4 methods tend to produce longer Rg-H+ distance than the CCSD(T) level value, and the CCSD-calculated Rg-H+ bond lengths are slightly shorter. DFT method is not reliable to study weak interaction in the OCH+-He and OCH+-Ne complexes. A qualitative result can be obtained for OCH+-Ar complex by using the DFT method; however, a higher-level method using a larger basis set is required for the quantitative predictions. For heavier atom (Kr, Xe)-containing complexes, only the CCSD method predicted longer Rg-H+ distance than that obtained at the CCSD(T) level. The DFT method can be applied to obtain the semiquantitative results. The relativistic effects are expected to have minor effect on the geometrical parameters, the H+-C stretching mode, and the dissociation energy. However, the dissociation energies are sensitive to the quality of the basis set. The nature of interaction between the OCH+ ion and Rg atoms was also analyzed in terms of the interaction energy components.

scholarly journals Density Functional Theory and Complete Basis Set Ab Initio Computational Study of Five-, Six-, Seven- and Eight-hydrogen Coordinated Carbon Cations

1999 ◽  
Vol 23 (8) ◽  
pp. 502-503
Author(s):  
Branko S. Jursic
Keyword(s):  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Computational Study ◽  
Basis Set ◽  
Functional Theory ◽  
Complete Basis ◽  
Complete Basis Set ◽  
High Level

High level ab initio and density functional theory studies are performed on highly protonated methane species.

Ab initio predictions of the zero field splittings and the singlet–triplet transition strengths for the n → π* transition of selenoformaldehyde

1993 ◽  
Vol 71 (10) ◽  
pp. 1706-1712 ◽  
Author(s):  
D.C. Moule ◽  
L. Chantranupong ◽  
R.H. Judge ◽  
D.J. Clouthier
Keyword(s):  
Energy Levels ◽  
Random Phase ◽  
Open Shell ◽  
Oscillator Strengths ◽  
Basis Set ◽  
Zero Field ◽  
Zero Field Splitting ◽  
Hartree Fock ◽  
Lower Valence ◽  
Polarization Functions

The energy levels of the lower valence and Rydberg states of selenoformaldehyde, CH2Se, have been calculated by the SCF/CI method. Wavefunctions for the ROHF (restricted open shell Hartree–Fock) states were obtained with the Binnings–Curtis double-ζ basis set, augmented with Rydberg and polarization functions. Configuration interaction was applied to the parent configurations, PCMO (parent configuration molecular orbital). Oscillator strengths were evaluated for the allowed electric dipole transitions by the RPA (random phase approximation), and SOPPA (second-order polarization propagator approximation) methods. The spin-orbit contribution to the zero field splitting of the first triplet state, 3A2(n,π*) as well as the oscillator strengths to the three spin components were calculated by perturbation theory. These calculations predict that the Sx, Sy, and Sz components are shifted by −96.091,−96.707, and + 29.167 cm−1, respectively, from their unperturbed position. The oscillator strengths for the three components fx, fy, and fz of the 3A2(n,π*) ← 1A1(g.s.) transition were calculated to be 3.45 × 10−7, 1.15 × 10−7, and 173.0 × 10−7.

Computational study of polarizability anisotropies

2018 ◽  
Vol 96 (10) ◽  
pp. 934-938
Author(s):  
Delano P. Chong
Keyword(s):  
Small Molecules ◽  
Density Functional ◽  
Computational Study ◽  
Chem Phys ◽  
Basis Set ◽  
Functional Theory ◽  
Exchange Correlation ◽  
Exchange Correlation Potential ◽  
Correlation Potential ◽  
Definition Of

The dipole polarizabilities (α) and polarizability anisotropies (Δα) of over 20 molecules are calculated to search for negative Δα. The geometry of each molecule is first optimized at the level of CCSD(T)/cc-pVQZ. Then, the α tensors are computed both with CCSD(T)/daug-cc-pVTZ in Gaussian 09 and with the exchange-correlation potential Vxc known as SAOP in the Amsterdam density functional theory program called ADF and a large basis set called QZ3P-3DIFFUSE. In addition to the popular formula of the ΔαRaman connected with Raman spectroscopy, we also present values of an alternative definition of the polarizability anisotropy ΔαKerr connected with Kerr spectroscopy, recently proposed by Kampfrath and colleagues (2018. Chem. Phys. Lett. 692: 319). On one hand, the signs of many ΔαRaman are undetermined; on the other hand, we obtain negative ΔαKerr for more than one-half of the small molecules studied. Of the 24 molecules studied, 18 have negative ΔαKerr.

scholarly journals Optical Properties of Silver-Mediated DNA from Molecular Dynamics and Time Dependent Density Functional Theory

2018 ◽  
Vol 19 (8) ◽  
pp. 2346 ◽  
Author(s):  
Esko Makkonen ◽  
Patrick Rinke ◽  
Olga Lopez-Acevedo ◽  
Xi Chen
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Time Dependent ◽  
Basis Set ◽  
Dna Nanostructures ◽  
Exchange Correlation ◽  
Hartree Fock ◽  
Spurious Peak ◽  
20 Nm ◽  
Dependent Density

We report a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics and time-dependent density functional (TDDFT) study of metal-mediated deoxyribonucleic acid (M-DNA) nanostructures. For the Ag + -mediated guanine tetramer, we found the maug-cc-pvdz basis set to be sufficient for calculating electronic circular dichroism (ECD) spectra. Our calculations further show that the B3LYP, CAM-B3LYP, B3LYP*, and PBE exchange-correlation functionals are all able to predict negative peaks in the measured ECD spectra within a 20 nm range. However, a spurious positive peak is present in the CAM-B3LYP ECD spectra. We trace the origins of this spurious peak and find that is likely due to the sensitivity of silver atoms to the amount of Hartree–Fock exchange in the exchange-correlation functional. Our presented approach provides guidance for future computational investigations of other Ag + -mediated DNA species.

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