Pseudopotentials for second row atoms. Abinitio molecular calculations on PH3, H2S, and HCl

1985 ◽  
Vol 63 (7) ◽  
pp. 1922-1924 ◽  
Author(s):  
Rezső Gáspár ◽  
Rezső Gáspár Jr.
Keyword(s):  
Dipole Moments ◽  
Substantial Reduction ◽  
Binding Energies ◽  
Force Constants ◽  
Ionization Potentials ◽  
Basis Set ◽  
Pseudopotential Method ◽  
Bond Angles ◽  
Bond Lengths ◽  
Molecular Calculations

Gaussian nonlocal pseudopotentials are introduced for the simplification of the description of second row elements. Pseudopotential parameters for P, S, and Cl are presented. The pseudopotential method is applied to HCl, H2S, and PH3. Substantial reduction in the dimension of the orbital basis set is achieved. Results on total valence energies, binding energies, ionization potentials, force constants, equilibrium bond angles, bond lengths, and dipole moments are presented and compared to experiment as well as to the results of calculations with other methods.

Notizen: Schwingungsspektren der Gold(I)-halogenide AuX (X = Cl, Br und I); Strukturprognosen für AuCl und AuBr / Vibrational Spectra of the Aurous Halides AuX (X= Cl, Br and I); Structural Prognoses for AuCl and AuBr

1974 ◽  
Vol 29 (11-12) ◽  
pp. 806-807 ◽  
Author(s):  
Dietrich Breitinger ◽  
Heiko Leuchtenstern
Keyword(s):  
Vibrational Spectra ◽  
Chain Structure ◽  
Force Constants ◽  
Bond Angles ◽  
Bond Lengths

Chain structure, Force constantsFrom vibrational spectra chain structures are predicted for AuCl and AuBr; bond angles, bond lengths and force constants have been estimated for these aurous halides.

Intermolecular π/π and H/π interactions in dimers researched by different computational methods

2014 ◽  
Vol 13 (07) ◽  
pp. 1450057
Author(s):  
Cuihong Wang ◽  
Yue Jiang ◽  
Ruiqin Zhang ◽  
Zijing Lin
Keyword(s):  
High Efficiency ◽  
Dipole Moments ◽  
Binding Energies ◽  
Basis Set ◽  
Theoretical Research ◽  
Basis Sets ◽  
Π Interactions ◽  
Π Stacking ◽  
Structures And Properties ◽  
Satisfactory Precision

The analysis of π/π and H /π interactions in complexes are a challenging aspect of theoretical research. Due to the different approximations of different levels of theory, results tend to be inconsistent. We compared the reliabilities of HF, SVWN, M06L, PW91, BLYP, B3LYP, BHandHLYP, B97D, MP2, and DFTB-D approaches in researching π/π and H /π interactions by calculating the binding energies of five benzene-containing dimers. The effects of 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results were analyzed too. We found that the DFTB-D and B97D methods combined with the 6-311++G** basis set perform well for dimers that contain π/π and H /π interactions. With high efficiency and satisfactory precision, DFTB-D is helpful for the calculation of complexes containing π/π and H /π stacking. We further calculated the structures and properties of phenylalanine-containing dimers using the DFTB-D and B97D methods. The properties of low energy conformers such as rotational constants, dipole moments and molecular orbitals were also analyzed. These data should be helpful for research into systems that contain π/π and H /π stacking.

scholarly journals Selection the Drug Efficacy of Oroidin Derivatives as Hsp90 Inhibitors by Computer Aided Drug Design Method

2020 ◽  
pp. 630-651
Author(s):  
Subhajit Sarkar ◽  
Rajesh Kumar Das
Keyword(s):  
Chemical Potential ◽  
Design Method ◽  
Molecular Descriptor ◽  
Dipole Moments ◽  
Binding Energies ◽  
Basis Set ◽  
Toxicity Tests ◽  
In Vitro Test ◽  
In Silico Studies

Heat shock protein 90 (Hsp90) is a conserved molecular chaperone associated with regulation of hundreds of client proteins that are key drivers, regulators and promoters of numerous refractory diseases including cancer. Consequently, Hsp90 is a significant target for the development of harmless anticancer therapies. Marine organisms are the rich source of pharmacological important compounds, especially oroidin. Oroidin, a pyrrole-2-aminoimidazole alkaloid, isolated from the marine sponge Agelas oroides, binds ATP pocket of Hsp90 and suppresses the ATPase activity of the protein. Natural product oroidin was selected as potent inhibitor of Hsp90 and its drug candidature was accordingly improved by substituting various functional groups. Virtual screenings were done through in silico studies, carried out on thirty nine derivatives of oroidin. DFT study was performed with Gaussian16, UB3LYP/6-311G++ (d, p) basis set to investigate the quantum mechanical parameters such as HOMO-LUMO energies, dipole moments. Derived parameters like ionization potential, electron affinity, softness-hardness, chemical potential and electrophilicity index were also calculated. Using AutoDock 4.0 programme, we studied docking of the thirty-nine designed derivatives with macromolecule Hsp90 and recorded the binding energy values of the best conformation out of nine in each docked compound. ADME predictions, molecular descriptor properties, and theoretical toxicity tests were evaluated using preADMET, molinspiration, and OSIRIS property explorer web tools respectively. We found twenty eight derived compounds, each docked at the same region of Hsp90, possessing higher binding energies compare to the precursor oroidin. Seven of them qualified all the rules of drug candidature and could be safe in using as effective drugs for cancer treatment. This study suggests that these compounds could be synthesized for in vitro test and may leads to a novel anticancer therapeutics.

A COMPARATIVE STUDY ON INTERMOLECULAR HYDROGEN BOND INTERACTIONS IN MOLECULAR DIMERS USING DIFFERENT LEVELS OF COMPUTATIONAL METHODS

2012 ◽  
Vol 11 (06) ◽  
pp. 1237-1259 ◽  
Author(s):  
CUIHONG WANG ◽  
RUIQIN ZHANG ◽  
ZIJING LIN
Keyword(s):  
Hydrogen Bond ◽  
High Efficiency ◽  
Intermolecular Hydrogen Bond ◽  
Good Choice ◽  
Binding Energies ◽  
Basis Set ◽  
Basis Sets ◽  
Bond Lengths ◽  
Hydrogen Bond Interactions ◽  
Theoretical Approaches

Hydrogen bond interactions in biological systems are important scientific issues but are challenging for their theoretical determinations at quantum-mechanical level of theory. Due to the different approximations, the available theoretical approaches often predict diverse hydrogen bond lengths and strengths. In this work, we evaluated the reliabilities of a number of widely used theoretical approaches including HF, SVWN, BLYP, PW91, B3LYP, BH and HLYP, B97D, M06L, MP2, and DFTB-D in studying hydrogen bonding, by calculating the hydrogen bond lengths and binding energies of 23 dimers formed by HCOOH , NH3 and Glycine. We also compared the effects of STO-3G, 6-31+G**, 6-311++G** and 6-311++G(2df,2p) basis sets on the results. Our result shows that, M06L, B3LYP and BHandHLYP methods can predict accurate dimer structures with a moderate basis set. Moreover, DFTB-D also gives reasonably reliable results with high efficiency and satisfactory precision, being a good choice for studying complex structures which contain hydrogen bonds.

Theoretical Study for the Interaction of Chitosan and Sulfate

2011 ◽  
Vol 695 ◽  
pp. 158-161
Author(s):  
Juan Qin Xue ◽  
Xiao Na Ma ◽  
Yu Jie Wang ◽  
Dan Dan Wen ◽  
Jun Yang
Keyword(s):  
Comparative Analysis ◽  
Density Functional ◽  
Theoretical Study ◽  
Binding Energies ◽  
Bond Angles ◽  
Bond Lengths ◽  
Carbon Ring ◽  
B3lyp Method ◽  
Adsorption Mode ◽  
Before And After

Choosing the basis of 6-311++G (d. p) with chitosan as its model, we use the density functional B3LYP method to optimize the structure and calculate the energy for the chitosan and sulfate. We study the adsorption for the sulfate from different adsorption point (amidogen, hydroxide and carbon-ring) with or without the protonation of chitosan amidogen. Through a comparative analysis of the bond-lengths, bond-angles, charges and binding energies before and after the interaction of chitosan and sulfate, we find that the adsorption of chitosan for sulfate is mainly the adsorption of amidogen after protonation. The adsorption mode is the combination of sulfate with two amidogens after protonation.

Divergence of Many-Body Perturbation Theory for Noncovalent Interactions of Large Molecules

2019 ◽  
Author(s):  
Brian Nguyen ◽  
Guo P Chen ◽  
Matthew M. Agee ◽  
Asbjörn M. Burow ◽  
Matthew Tang ◽  
...  
Keyword(s):  
Perturbation Theory ◽  
System Size ◽  
State Density ◽  
Second Order ◽  
Binding Energies ◽  
Basis Set ◽  
Many Body ◽  
Many Body Perturbation Theory ◽  
Relative Errors ◽  
Ground State Density

Prompted by recent reports of large errors in noncovalent interaction (NI) energies obtained from many-body perturbation theory (MBPT), we compare the performance of second-order Møller–Plesset MBPT (MP2), spin-scaled MP2, dispersion-corrected semilocal density functional approximations (DFA), and the post-Kohn–Sham random phase approximation (RPA) for predicting binding energies of supramolecular complexes contained in the S66, L7, and S30L benchmarks. All binding energies are extrapolated to the basis set limit, corrected for basis set superposition errors, and compared to reference results of the domain-based local pair-natural orbital coupled-cluster (DLPNO-CCSD(T)) or better quality. Our results confirm that MP2 severely overestimates binding energies of large complexes, producing relative errors of over 100% for several benchmark compounds. RPA relative errors consistently range between 5-10%, significantly less than reported previously using smaller basis sets, whereas spin-scaled MP2 methods show limitations similar to MP2, albeit less pronounced, and empirically dispersion-corrected DFAs perform almost as well as RPA. Regression analysis reveals a systematic increase of relative MP2 binding energy errors with the system size at a rate of approximately 1‰ per valence electron, whereas the RPA and dispersion-corrected DFA relative errors are virtually independent of the system size. These observations are corroborated by a comparison of computed rotational constants of organic molecules to gas-phase spectroscopy data contained in the ROT34 benchmark. To analyze these results, an asymptotic adiabatic connection symmetry-adapted perturbation theory (AC-SAPT) is developed which uses monomers at full coupling whose ground-state density is constrained to the ground-state density of the complex. Using the fluctuation–dissipation theorem, we obtain a nonperturbative “screened second-order” expression for the dispersion energy in terms of monomer quantities which is exact for non-overlapping subsystems and free of induction terms; a first-order RPA-like approximation to the Hartree, exchange, and correlation kernel recovers the macroscopic Lifshitz limit. The AC-SAPT expansion of the interaction energy is obtained from Taylor expansion of the coupling strength integrand. Explicit expressions for the convergence radius of the AC-SAPT series are derived within RPA and MBPT and numerically evaluated. Whereas the AC-SAPT expansion is always convergent for nondegenerate monomers when RPA is used, it is found to spuriously diverge for second-order MBPT, except for the smallest and least polarizable monomers. The divergence of the AC-SAPT series within MBPT is numerically confirmed within RPA; prior numerical results on the convergence of the SAPT expansion for MBPT methods are revisited and support this conclusion once sufficiently high orders are included. The cause of the failure of MBPT methods for NIs of large systems is missing or incomplete “electrodynamic” screening of the Coulomb interaction due to induced particle–hole pairs between electrons in different monomers, leaving the effective interaction too strong for AC-SAPT to converge. Hence, MBPT cannot be considered reliable for quantitative predictions of NIs, even in moderately polarizable molecules with a few tens of atoms. The failure to accurately account for electrodynamic polarization makes MBPT qualitatively unsuitable for applications such as NIs of nanostructures, macromolecules, and soft materials; more robust non-perturbative approaches such as RPA or coupled cluster methods should be used instead whenever possible.<br>

Vibrational spectra of aquadioxotetra; peroxodivanadates(V) M2[V2O2(O2)4(H2O)]·xH2O (M = N(CH3)4, Cs)

1990 ◽  
Vol 55 (6) ◽  
pp. 1485-1490 ◽  
Author(s):  
Peter Schwendt ◽  
Milan Sýkora
Keyword(s):  
Raman Spectra ◽  
Vibrational Spectra ◽  
Normal Coordinate Analysis ◽  
Force Constants ◽  
Infrared And Raman Spectra ◽  
Empirical Correlations ◽  
Normal Coordinate ◽  
Bond Lengths ◽  
Stretching Vibrations

The infrared and Raman spectra of M2[V2O2(O2)4(H2O)]·xH2O and M2[V2O2(O2)4(D2O)]·xD2O (M = N(CH3)4, Cs) were measured. In the region of the vanadium-oxygen stretching vibrations, the spectra were interpreted based on normal coordinate analysis, employing empirical correlations between the bond lengths and force constants.

Synthesis and Crystal Structures of Three Carboxylate- Bridged Tetranuclear Copper(II) - Lanthanide(III) Complexes of Ph3P+CH2CH2CO2−

1999 ◽  
Vol 52 (10) ◽  
pp. 983 ◽  
Author(s):  
Yang-Yi Yang ◽  
Seik Weng Ng ◽  
Xiao-Ming Chen
Keyword(s):  
Oxygen Atom ◽  
Crystal Structures ◽  
Triclinic Space Group ◽  
Coordination Environment ◽  
Space Group ◽  
Bond Angles ◽  
Bond Lengths ◽  
Metal Atoms ◽  
Apical Site

Three tetranuclear copper(II)–lanthanide(III) complexes of triphenylphosphoniopropionate (Ph3P+CH2CH2CO2−,tppp), namely [Cu2Ln2(tppp)8(H2O)8](ClO4)10·2H 2 O [Ln = EuIII, NdIII or CeIII], were synthesized and characterized by crystallography. The EuIII complex crystallizes in the triclinic space group P1 – with a 16.249(7), b 17.185(11), c 17.807(11) Å, α 69.750(10), β 89.230(10), γ 84.070(10)˚, V 4639(5) Å3, Z 1. In the crystal structures, four tppp ligands bridge a pair of CuII and tetraaquo-EuIII atoms (Cu···Eu 3.527(2) Å) through their µ2-carboxylato ends to form a dinuclear subunit; two of these subunits are additionally linked by one of the CuII -bonded carboxylato oxygen ends, across a centre of inversion, to furnish a dimeric tetranuclear [Cu(tppp)4 Eu(H2O)4]2 species (Cu···Cu 3.323(2) Å). This CuII -bonded oxygen atom occupies the apical site of the square-pyramidal coordination environment of the CuII atom. The EuIII atom is eight-coordinated in a square-antiprismatic geometry. The NdIII and CeIII complexes are isomorphous to the EuIII complex, and only minor differences in bond lengths and bond angles involving the metal atoms are noted.

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