Automatic geometry optimization for molecules withd orbitals. I. General analytic formulas for derivatives of slater orbitals

1978 ◽  
Vol 13 (2) ◽  
pp. 227-233 ◽  
Author(s):  
S. Beran ◽  
Z. Slanina ◽  
D. C. Zidarov
Keyword(s):  
Geometry Optimization ◽  
Slater Orbitals ◽  
Derivatives Of

Syntheses, geometry optimization, and electronic structure of N-and C-substituted benzonaphthyridines

2006 ◽  
Vol 60 (1) ◽  
Author(s):  
M. Deska ◽  
W. Śliwa
Keyword(s):  
Electronic Structure ◽  
Ab Initio ◽  
13C Nmr ◽  
Effective Charge ◽  
Nmr Spectra ◽  
Geometry Optimization ◽  
13C Nmr Spectra ◽  
Derivatives Of ◽  
Hydroxyethyl Group

AbstractSynthesis of N-and C-substituted derivatives of benzo[h][1,6]naphthyridine, bearing 2-hydroxyethyl group has been made by quaternization reaction and by condensation of corresponding methylbenzonaphthyridines with formaldehyde. For six derivatives of isomeric benzo[c][1,5]-, benzo[h][1,6]-, and benzo[f][1,7]naphthyridines the 13C NMR spectra are discussed.For ten compounds the geometry was optimized with the AM1 and, in one case also with the ab initio 6–31G method; their effective charge values have also been calculated.

scholarly journals Geometry Optimization Speedup Through a Geodesic Approach to Internal Coordinates

2021 ◽  
Author(s):  
Eric Hermes ◽  
Khachik Sargsyan ◽  
Habib Najm ◽  
Judit Zádor
Keyword(s):  
Differential Equation ◽  
Ordinary Differential Equation ◽  
Displacement Vector ◽  
Geometry Optimization ◽  
Molecular Geometry ◽  
Internal Coordinates ◽  
Derivatives Of

We present a new geodesic-based method for geometry optimization in a basis of redundant internal coordinates. Our method updates the molecular geometry by following the geodesic generated by a displacement vector on the internal coordinate manifold, which dramatically reduces the number of steps required to reach convergence. Our method can be implemented in any existing optimization code, requiring only implementation of derivatives of the Wilson B-matrix and the ability to solve an ordinary differential equation.

scholarly journals Geometry Optimization Speedup Through a Geodesic Approach to Internal Coordinate Optimization

2021 ◽  
Author(s):  
Eric Hermes ◽  
Khachik Sargsyan ◽  
Habib Najm ◽  
Judit Zádor
Keyword(s):  
Molecular Structure ◽  
Differential Equation ◽  
Ordinary Differential Equation ◽  
Newton Method ◽  
Displacement Vector ◽  
Geometry Optimization ◽  
Internal Coordinates ◽  
Derivatives Of ◽  
Method Approach

We present a new geodesic-based method for geometry optimization in a basis of redundant internal coordinates.<br>This method realizes displacements along internal coordinates by following the geodesic generated by the displacement vector on the internal coordinate manifold.<br>Compared to the traditional Newton method approach to taking displacements in internal coordinates, this geodesic approach substantially reduces the number of steps required to reach convergence on a molecular structure minimization benchmark.<br>This new geodesic method can in principle be implemented in any existing optimization code, and only requires the implementation of derivatives of the Wilson B-matrix and the ability to solve a relatively inexpensive ordinary differential equation.

Theoretical investigation of the conformational intricacies and thermodynamic functions of noradrenaline

2011 ◽  
Vol 89 (8) ◽  
pp. 1010-1020 ◽  
Author(s):  
DongJin R. Lee ◽  
Natalie J. Galant ◽  
Donghoon M. Lee ◽  
Sean S.H. Dawson ◽  
Vanna Z.Y. Ding ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Thermodynamic Functions ◽  
Adrenergic Receptor ◽  
Geometry Optimization ◽  
Hydroxyl Groups ◽  
Amino Acid Residues ◽  
Stable Conformation ◽  
Hartree Fock ◽  
First Time ◽  
Derivatives Of

Noradrenaline is a neurotransmitter that is involved in various psychological processes. In the neurotransmission process, noradrenaline binds to an adrenergic receptor by forming a complex of hydrogen bonds between its two catechol ring hydroxyl groups and the amino acid residues of adrenergic receptors. Although the two catechol ring hydroxyl groups play a crucial role in making hydrogen bonds to the binding site of the adrenergic receptor, the contribution of the catechol ring hydroxyl groups to the intramolecular stability that may affect docking has not been fully studied. To reveal the specific role that the catechol ring hydroxyl groups might play in stabilizing noradrenaline, the quantum chemical computations of geometry optimization and thermodynamic functions of N-protonated noradrenaline conformers were performed at both the B3LYP/6–31G(d,p) and G3MP2B3 levels of theory, using the Gaussian 03 program. The results were compared with those of N-protonated β-hydroxy-β-phenylethylamine, which is identical to noradrenaline except it lacks two catechol ring hydroxyl groups. For the first time, post-Hartree–Fock computations were used to obtain thermodynamic functions to establish relative stabilities of all possible conformers of N-protonated noradrenaline. In this study, 18 distinct structures of N-protonated noradrenaline were revealed, and the catechol ring hydroxyl groups were found to affect noradrenaline stability positively or negatively depending on the conformational orientations. On the basis of available experimental results, the issue that the least stable conformation of two catechol ring hydroxyl groups may be involved in the docking process has been raised. These findings may be useful in synthesis of derivatives of noradrenaline in drug design.

scholarly journals Calculating energy derivatives for quantum chemistry on a quantum computer

2019 ◽  
Vol 5 (1) ◽  
Author(s):  
Thomas E. O’Brien ◽  
Bruno Senjean ◽  
Ramiro Sagastizabal ◽  
Xavier Bonet-Monroig ◽  
Alicja Dutkiewicz ◽  
...  
Keyword(s):  
Bond Length ◽  
Quantum Computer ◽  
Survey Methods ◽  
Geometry Optimization ◽  
Equilibrium Bond Length ◽  
Molecular Systems ◽  
Energy Derivatives ◽  
Quantum Processor ◽  
Dynamics Simulations ◽  
Derivatives Of

AbstractModeling chemical reactions and complicated molecular systems has been proposed as the “killer application” of a future quantum computer. Accurate calculations of derivatives of molecular eigenenergies are essential toward this end, allowing for geometry optimization, transition state searches, predictions of the response to an applied electric or magnetic field, and molecular dynamics simulations. In this work, we survey methods to calculate energy derivatives, and present two new methods: one based on quantum phase estimation, the other on a low-order response approximation. We calculate asymptotic error bounds and approximate computational scalings for the methods presented. Implementing these methods, we perform geometry optimization on an experimental quantum processor, estimating the equilibrium bond length of the dihydrogen molecule to within $$0.014$$0.014 Å of the full configuration interaction value. Within the same experiment, we estimate the polarizability of the H$${}_{2}$$2 molecule, finding agreement at the equilibrium bond length to within $$0.06$$0.06 a.u. ($$2 \%$$2% relative error).

scholarly journals Antimycobacterial Activities of Ruthenium(II) Complexes of Hydroxyl Flavone Hydrazones

2020 ◽  
Vol 10 (1) ◽  
pp. 1760-1791
Keyword(s):  
Biological Activity ◽  
Geometry Optimization ◽  
Antimycobacterial Activity ◽  
Dna Interaction ◽  
Microtiter Plate ◽  
Spectroscopic Techniques ◽  
Microtiter Plate Assay ◽  
Hydrazine Derivatives ◽  
Colony Forming Unit ◽  
Derivatives Of

The Ru(II) complexes of hydrazine derivatives of different 3-hydroxy 4-substituted flavones was synthesized to assess their biological activity. The ligand 2, 4 dinitrophenyl hydrazones of 3-hydroxy 4´-substituted flavones [where 4´-substituents are -OCH3(HL1), -NO2(HL2), NMe2(HL3), Cl (HL4), OCH2Ph (HL5)] were successfully coordinated with Ru(phen)2Cl2 which consists of the formula, [Ru(phen)2(HL1)]Cl2.2.5H2O (M1R), [Ru(phen)2(HL2)]Cl2(M2R), [Ru(phen)2(HL3)]Cl2(M3R), [Ru(phen)2(HL4)]Cl2.1.5H2O (M4R), [Ru(phen)2(HL5)]Cl2.1.5H2O (M5R). All the synthesized complexes were characterized by elemental analysis, IR, 1H-NMR, UV-Vis, and ESI-MS spectroscopic techniques. The geometry optimization of all complexes was carried by using Gaussian-09. All compounds were studied for antimycobacterial activity using Resazurin microtiter plate assay (REMA) followed by colony-forming unit (CFU) count. The metal complexes showed promising activity against M. smegmatis mc2. The DNA interaction of the complexes was also studied. These studies suggest that hydrazine derivatives of 3-hydroxy 4-substituted flavones and their Ru(II) complexes can be good candidates for antimycobacterial drug development studies.

Molecular Structure and UV Absorption Spectra of OH and NH2 Derivatives of Dodecamethylcyclohexasilane: A Combined Experimental and Computational Study

2009 ◽  
Vol 64 (11-12) ◽  
pp. 1598-1606 ◽  
Author(s):  
Harald Stueger ◽  
Gottfried Fuerpass ◽  
Judith Baumgartner ◽  
Thomas Mitterfellner ◽  
Michaela Flock
Keyword(s):  
Absorption Spectra ◽  
Computational Study ◽  
Geometry Optimization ◽  
Chair Conformation ◽  
Uv Absorption ◽  
Equatorial Position ◽  
Full Geometry Optimization ◽  
Uv Absorption Spectra ◽  
X Ray Crystallography ◽  
Derivatives Of

The monofunctionalized cyclohexasilanes XSi6Me11 [X = -OH (2); -NH2 (3)] are easily accessible from XSi6Me11 and H2O/Et3N or NH3, respectively. The crystal structure of 2 as determined by single crystal X-ray crystallography exhibits the cyclohexasilane ring in chair conformation with the OH group in an unusual equatorial position due to intermolecular hydrogen bonding. Full geometry optimization (B3LYP/6-31+G∗) of the gas-phase structures of 2 and 3 affords six minima on the potential energy surface for chair, twist and boat conformers with the heterosubstituents either in axial or equatorial positions all being very close in energy. According to time-dependent DFT B3LYP/TZVP calculations contributions of several conformers to the observed solution UV absorption spectra of dodecamethylcyclohexasilane (1), 2 and 3 need to be considered in order to achieve satisfactory agreement of calculated and experimental data

scholarly journals Geometry Optimization Speedup Through a Geodesic Approach to Internal Coordinate Optimization

2021 ◽  
Author(s):  
Eric Hermes ◽  
Khachik Sargsyan ◽  
Habib Najm ◽  
Judit Zádor
Keyword(s):  
Molecular Structure ◽  
Differential Equation ◽  
Ordinary Differential Equation ◽  
Newton Method ◽  
Displacement Vector ◽  
Geometry Optimization ◽  
Internal Coordinates ◽  
Derivatives Of ◽  
Method Approach

We present a new geodesic-based method for geometry optimization in a basis of redundant internal coordinates.<br>This method realizes displacements along internal coordinates by following the geodesic generated by the displacement vector on the internal coordinate manifold.<br>Compared to the traditional Newton method approach to taking displacements in internal coordinates, this geodesic approach substantially reduces the number of steps required to reach convergence on a molecular structure minimization benchmark.<br>This new geodesic method can in principle be implemented in any existing optimization code, and only requires the implementation of derivatives of the Wilson B-matrix and the ability to solve a relatively inexpensive ordinary differential equation.

Sign in / Sign up

Export Citation Format

Share Document