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Theoretical studies on adsorption of organic molecules on metal surface
Published in Tanmoy Chakraborty, Prabhat Ranjan, Anand Pandey, Computational Chemistry Methodology in Structural Biology and Materials Sciences, 2017
where, ∇ee(G - G), ∇ve(G - G) and ∇XC(G - G) are the Fourier transforms of electron-electron, electron-nuclei and exchange correlation potentials. Plane waves have a number of advantages because,It is easy to calculate all kinds of matrix elements through fast Fourier transform techniques.The size ofbasis set can be increased systematically in a simple way.The same basis set can be used for all atomic species.Forces acting on atoms are equal to Hellmann-Feynman forces.Convergence towards completeness can be tested.The plane waves do not depend on nuclear positions, so unlike localized basis sets, correlation terms are not needed for the calculation of forces.Plane wave basis sets are free from ‘basis set superposition error’(BSSE).
Computational Modeling and Theoretical Strategies for the Design of Chiral Recognition Sites Using Molecular Imprinting Technology
Published in Didier Rouxel, Sabu Thomas, Nandakumar Kalarikkal, Sajith T. Abdulrahman, Advanced Polymeric Materials, 2022
T. Sajini, Aravind Krishnan, Beena Mathew
The self-consistent reaction field of Tomasi PCM was used by Junbo Liu et al. to simulate the interactions among Dicyandiamide (DCD), the template molecule, and MAA as well as DCD and different cross-linkers in ACN solution at 333 K [26]. The binding energy between DCD and the functional monomer (DEB1) was calculated using the Equation (10.1): ΔEB1=Etemplate − monomer −Etemplate −ΣEmonomer where Etemplate-monomer is the energy of template and monomer, Etemplate represents the energy of template, and ΣEmonomer means the sum of energy for monomer. The binding energy between the template and cross-linker (ΔEB2) was calculated using the Equation (10.2): ΔEB2=Etemplate-cross-linker −Etemplate −Ecross-linker where Etemplate-cross-linker is the energy of template and cross-linker, Etemplate represents the energy of template, and Ecross-linker means the energy of cross-linker. The binding energy between monomer and cross-linker (ΔEB3) was calculated using the Equation (10.3). ΔEB3=Emonomer-cross-linker −Emonomer −Ecross-linker where Etemplate-cross-linker is the energy of template and cross-linker, Emonomer represents the energy of monomer, and Ecross-linker means the energy of cross-linker. Moreover, the basis set superposition error (BSSE) was taken into account through counterpoise correction method.
Interaction of moderately reactive molecules with organic superhalogens: a theoretical perspective
Published in Molecular Physics, 2020
Subhendu Sarkar, Tamalika Ash, Tanay Debnath, Abhijit K. Das
Gaussian 09 [39] suite of quantum chemistry program has been used to perform first principle density functional theory calculations. The optimization of the moderately reactive molecules, superhalogen moieties and the MRM–OSH complexes has been carried out using M06-2X [40], B3LYP [41,42] and ωB97XD [43] methods in conjunction with the cc-pVTZ [44,45] basis set. The basis set superposition error (BSSE) has been taken into account by the counterpoise procedure [46]. The choice of M06-2X method is dictated by the fact that it is suitable for main-group thermochemistry and non-covalent interactions [40]. As the M06-2X functional is highly non-local and takes into account the double of non-local exchange (2X) [40], it gives better result compared to both the B3LYP and ωB97XD methods. So, we carried out our calculations using the M06-2X method only. The results obtained using ωB97XD and B3LYP methods are provided in the supplementary information. The optimised structures of OSHs, MRMs and the MRM–OSH complexes have been obtained without any imaginary frequency. The expression for calculating BE value is as follows: where E(species) stands for the zero-point-corrected energy evaluated with optimised geometries.
On the origin of bonding in metals: lithium as a case study
Published in Molecular Physics, 2022
The basis sets adopted are uncontracted Gaussian type functions (GTF). A small basis set , and two large basis sets and . Our integral code requires family type basis sets. Further, the exponents are all drawn from the same set of universal type exponents, i.e. . The parameters defining the basis sets are given in Table 1.
Dipole orientation variation of hydration shell around alkali metal cation on hexagonal boron nitride sheet
Published in Molecular Physics, 2021
Junwei Yang, Jige Chen, Haiping Fang
A h-BN sheet (48 boron atoms, 48 nitrogen atoms and 24 hydrogen atoms) was used in Figure 1(a). The initial structures of cation-(H2O)n complexes on the h-BN sheet and cation-(H2O)n complexes in vacuum were produced by ABCluster software [37,38]. The ABCluster software can search the global as well as the local minima of clusters or complexes by the (ABC) algorithm. To ensure reliability, 500 initial structures for cation-(H2O)n complexes on the h-BN sheet and cation-(H2O)n complexes in vacuum will be generated and pre-optimised by the semiempirical tight-binding based quantum chemistry method [39,40], respectively. After excluding the same and scattered structures of cation-(H2O)n complexes on the h-BN sheet and in vacuum, we selected 20 of the minimum energy structures for each n to subsequent optimisation. Then, geometry optimisations of 20 minimum energy structures were performed by Gaussian 09 program [41]. The h-BN sheet was flexible. They were fully optimised by B3LYP-D3(BJ) method for dispersion correction [42] with Becke–Johnson damping [43] using the 6-31G(d) basis in the framework of DFT. This basis has been widely used to investigate cation-π and hydrated cation-π interaction [19,44–47]. In the optimisation steps, the Berny algorithm [48] was used with the convergence criteria of a maximum step size of 0.0018 au and a root mean square (RMS) force of 0.0003 au. The basis set superposition error (BSSE) corrections were obtained by the counterpoise method [49]. Most stable and metastable optimised structures were obtained from geometry optimisations; metastable optimised structure denotes local minima. Vibrational frequency of these optimised structures was calculated to confirm their stability without imaginary frequency. The models and methods also were used to investigate interaction of alkali metal cation with the h-BN sheet (please see PS1 in the Supporting Information).