Sarah L V Zahn, Ole Hammerich, Poul Erik Hansen, Stephan P A Sauer
The prediction of 13 C chemical shifts can be challenging with density functional theory (DFT). In this study 39 different functionals and three different basis sets were tested on three neutral alkylpyrroles and their corresponding protonated species. The calculated shielding constants were compared to experimental data and results from previous calculations at the MP2. We find that the meta-hybrid functional TPSSh with either the Pople style basis set 6-311++G(2d,p) or the polarization consistent basis set pcSseg-1 gives the best results for the 13 C chemical shifts, whereas for the 1 H chemical shifts it is the TPSSh functional with either the 6-311++G(2d,p) or pcSseg-2 basis set...
April 30, 2021: Journal of Computational Chemistry
Ryan S DeFever, Ray A Matsumoto, Alexander W Dowling, Peter T Cummings, Edward J Maginn
We introduce a new Python interface for the Cassandra Monte Carlo software, molecular simulation design framework (MoSDeF) Cassandra. MoSDeF Cassandra provides a simplified user interface, offers broader interoperability with other molecular simulation codes, enables the construction of programmatic and reproducible molecular simulation workflows, and builds the infrastructure necessary for high-throughput Monte Carlo studies. Many of the capabilities of MoSDeF Cassandra are enabled via tight integration with MoSDeF...
April 30, 2021: Journal of Computational Chemistry
Abdelmalek Khorief Nacereddine, Lynda Merzoud, Christophe Morell, Henry Chermette
The selectivity and the mechanism of the uncatalyzed and AlCl3 catalyzed hetero-Diels-Alder reaction (HDR) between ([E]-4-methylpenta-2,4-dienyloxy)(tert-butyl)dimethylsilane 1 and benzaldehyde 2 have been studied using density functional theory at the MPWB1K/6-31G(d) level of theory. The uncatalyzed HDR between diene 1 and alkene 2 is characterized by a polar character and proceeds via an asynchronous one-step mechanism for the meta paths and synchronous for the ortho ones. In the presence of AlCl3 catalyst, the mechanism changes to be stepwise, while the first step is the rate-determining step...
April 30, 2021: Journal of Computational Chemistry
Jorge I Martínez-Araya, Christophe Morell
Some Mo-oxo complexes bearing pyridine rings have the capability for dihydrogen production from water. However, energy barrier and overall energy vary depending on the effect exerted by several substituent groups located at different positions around one or more pyridine rings which are ligands of these compounds. Based on the Karunadasa and coworkers investigation where the para-position was experimentally tested in compounds derivatised from the 2,6-bis[1,1-bis(2-pyridil)ethyl]-pyridine oxo-molybdenum complex synthesized (Karunadasa et al...
April 20, 2021: Journal of Computational Chemistry
Gabriela Dias-da-Silva, Rodrigo L O R Cunha, Mauricio D Coutinho-Neto
There have been significant advances in the biological use of hypervalent selenium and tellurium compounds as cysteine protease inhibitors. However, the full understanding of their reaction mechanisms for and cysteine proteases inhibition is still elusive. Kinetic studies suggest an irreversible inhibition mechanism, which was explained by forming a covalent bond between the enzyme sulfhydryl group and the chalcogen atom at its hypervalent state (+4). In this work, we performed a theoretical investigation using density functional theory to propose the active inhibitor form in an aqueous solution...
April 19, 2021: Journal of Computational Chemistry
Zaki S Safi, Nuha Wazzan
This study presents the benchmark calculations of proton affinities (PAs) and gas-phase basicities (GBs) of 8-para substituted benzaldehyde compounds using the multilevel model chemistries (G3B3 and G4), density-functional quantum model (B3LYP) and ab initio model (MP2). The results show that the computed properties are strongly correlated with the available experimental data. The PAs and the GBs of other eight para-substituted benzaldehyde compounds, for which the experimental data does not currently exist, have been calculated using G3B3 and B3LYP methods...
April 19, 2021: Journal of Computational Chemistry
Pirouz Kiani, Elaine S Dodsworth, A B P Lever, William J Pietro
Ligand electrochemical parameters, EL , more commonly known as Lever parameters, have played a major research role in understanding redox processes involved in inorganic electrochemistry, enzymatic reactions, catalysis, solar cells, biochemistry, and materials science. Despite their broad usefulness, Lever parameters are not well understood at a first-principles level. Using density functional theory, we demonstrate in this contribution that a ligand's Lever parameter is fundamentally related to the ligand's ability to alter the eigenvalue of the electroactive spin-orbital in an octahedral transition metal complex...
April 18, 2021: Journal of Computational Chemistry
Sai Manoj N V T Gorantla, Pattiyil Parameswaran, Kartik Chandra Mondal
The stability and bonding of a series of hetero-diatomic molecules with general formula (cAAC)EM(CO)n , where cAAC = cyclic alkyl(amino) carbene; E = group 14 elements (C, Si, and Ge); M = transition metal (Ni, Fe, and Cr) have been studied by quantum chemical calculations using density functional theory (DFT) and energy decomposition analysis-natural orbital chemical valence (EDA-NOCV). The equilibrium geometries were calculated at the BP86/def2-TZVPP level of theory. The tri-coordinated group 14 complex (1a, 4a, and 7a) in which one of the CO groups is migrated to the central group 14 element from adjacent metal is theoretically found to be more stable when the central atom (E) is carbon...
April 15, 2021: Journal of Computational Chemistry
Demeter Tzeli
Quadruple bonding is uncommon for main group elements and the identification of species forming such bonds is remarkably interesting particularly in diatomic anions for which there is a lack of information. Here, it is found that the MX- anions, TcN- , RuC- , RhB- , and PdBe- , present quadruple bonding, as do the corresponding MX neutrals, even though a different type of σ2 bond is involved in Σ+ states of neutral and anions. Specifically, the ground states (X2 Δ or X2 Σ+ ) of the four anions and their first excited states (A2 Σ+ or A2 Δ) of TcN- , RuC- , and RhB- present quadruple bonds consisting of two σ and two π bonds: (4dz2  - 2pz )2 , 5pz 0  ← 2s2 , (4dxz  - 2px )2 , and (4dyz  - 2py )2 ...
April 14, 2021: Journal of Computational Chemistry
Adyasa Priyadarsini, Bhabani S Mallik
The study of the water-splitting process, which can proceed in 2e- as well as 4e- pathway, reveals that the process is entirely an uphill process, and the third step, that is, the oxooxo bond formation is the rate-determining step. The kinetic barrier of the oxygen evolution reaction (OER) on the 2D material catalysts in the presence of explicit solvents is scarcely studied. Here, we investigate the dynamics of the OER on the undoped graphene and the activation energy barrier of each step using first principles molecular dynamics simulations...
April 13, 2021: Journal of Computational Chemistry
Xiangyu Jia, Hu Ge, Ye Mei
In the present study, the Divide and Conquer MBAR (DC-MBAR) method is proposed to predict the free energies based on the data sampled by multi-states simulations. For DC-MBAR method, the overlap between any two alchemical states is calculated first and those with sufficient overlap are defined as the adjacent states. Unlike the traditional MBAR method, which calculates the free energy of each state using all the data at once, DC-MBAR focuses on predicting the free energy changes between adjacent states. To estimate the free energy changes accurately, the other states with overlaps with the two adjacent states bigger than the defined threshold are included in the MBAR equation...
April 13, 2021: Journal of Computational Chemistry
Agnieszka Kącka-Zych, Radomir Jasiński
The reactions of γ-dehydronitration of furaxanenitrolic acids have been studied within the density functional theory using molecular electron density theory scheme at the MPWB1K(PCM)/6-311G(d,p) level of theory. The alteration of bonding along the course of the reaction is studied in the topology of the electron density functional within the bonding evolution theory perspective. The characteristics of electron density changes indicate that we can distinguish six different phases in the nitrous acid extrusion from furaxanenitrolic acid 1a...
April 12, 2021: Journal of Computational Chemistry
Ryan L Hayes, Charles L Brooks
Computation of the thermodynamic consequences of protein mutations holds great promise in protein biophysics and design. Alchemical free energy methods can give improved estimates of mutational free energies, and are already widely used in calculations of relative and absolute binding free energies in small molecule design problems. In principle, alchemical methods can address any amino acid mutation with an appropriate alchemical pathway, but identifying a strategy that produces such a path for proline and glycine mutations is an ongoing challenge...
April 12, 2021: Journal of Computational Chemistry
Sergei F Vyboishchikov, Alexander A Voityuk
We propose an efficient and accurate non-iterative method, dubbed uESE, for calculating solvation free energies. Apart from a COSMO-like electrostatic term, the model takes into account non-electrostatic contributions, which depend on atomic surfaces, induced surface charge densities, and the molecular volume. uESE is tested on 35 polar and 57 non-polar solvents. The calculated and experimental solvation free energies are compared for 2892 systems. The method exhibits an excellent performance, which is superior to major solvation methods...
April 12, 2021: Journal of Computational Chemistry
Raúl Palmeiro, Obis Castaño
The mechanism of 6-π electrocyclization of all-cis, mono-trans, and double-trans [10]annulene to yield 4a,8a-dihydronaphthalene has been explored at various quantum-chemical methods. The mono-trans configuration cyclizes preferentially to trans-4a,8a-dihydronaphthalene, in agreement with the experimental results. The cyclization of the all-cis configuration requires firstly a bond-shifting to the naphthalene-like conformation of double-trans [10]annulene, which is the rate-limiting step, and finally its azulene-like conformation electrocyclizes quickly to cis-4a,8a-dihydronaphthalene...
April 12, 2021: Journal of Computational Chemistry
Bernardino Tirri, Gloria Mazzone, Alistar Ottochian, Jerôme Gomar, Umberto Raucci, Carlo Adamo, Ilaria Ciofini
The combination of a Monte Carlo (MC) sampling of the configurational space with time dependent-density functional theory (TD-DFT) to estimate vertical excitations energies has been applied to compute the absorption spectra of a family of merocyanine dyes in both their monomeric and dimeric forms. These results have been compared to those obtained using a static DFT/TD-DFT approach as well as to the available experimental spectra. Though suffering of the limitations related to the use of DFT and TD-DFT for this type of systems, our data clearly show that the classical MC sampling provides a suitable alternative to classical molecular dynamics to explore the structural flexibility of these donor-acceptor (D-π-A) chromophores enabling a realistic description of the potential energy surface of both their monomers and aggregates (here dimers) and thus of their spectra...
April 2, 2021: Journal of Computational Chemistry
Joachim Laun, Thomas Bredow
Consistent basis sets of triple-zeta valence with polarization quality for the elements Cs-Po were derived for periodic quantum-chemical solid-state calculations. They are an extension of the pob-TZVP-rev2 [Vilela Oliveira, D.; Laun, J.; Peintinger, M. F. and Bredow, T., J. Comput. Chem., 2019, 40 (27), 2364-2376] basis sets and are based on the fully relativistic effective core potentials (ECPs) of the Stuttgart/Cologne group and on the def2-TZVP valence basis of the Ahlrichs group. The basis sets are constructed to minimize the basis set superposition error (BSSE) in crystalline systems...
March 31, 2021: Journal of Computational Chemistry
Nazanin Donyapour, Matthew Hirn, Alex Dickson
This work examines methods for predicting the partition coefficient (log P) for a dataset of small molecules. Here, we use atomic attributes such as radius and partial charge, which are typically used as force field parameters in classical molecular dynamics simulations. These atomic attributes are transformed into index-invariant molecular features using a recently developed method called geometric scattering for graphs (GSG). We call this approach "ClassicalGSG" and examine its performance under a broad range of conditions and hyperparameters...
March 30, 2021: Journal of Computational Chemistry
Yoshimichi Andoh, Shin-Ichi Ichikawa, Tatsuya Sakashita, Noriyuki Yoshii, Susumu Okazaki
In the era of exascale supercomputers, large-scale, and long-time molecular dynamics (MD) calculations are expected to make breakthroughs in various fields of science and technology. Here, we propose a new algorithm to improve the parallelization performance of message passing interface (MPI)-communication in the MPI-parallelized fast multipole method (FMM) combined with MD calculations under three-dimensional periodic boundary conditions. Our approach enables a drastic reduction in the amount of communication data, including the atomic coordinates and multipole coefficients, both of which are required to calculate the electrostatic interaction by using the FMM...
March 29, 2021: Journal of Computational Chemistry
Martyna Maszota-Zieleniak, Mateusz Marcisz, Małgorzata M Kogut, Till Siebenmorgen, Martin Zacharias, Sergey A Samsonov
Glycosaminoglycans (GAGs), long linear periodic anionic polysaccharides, are key molecules in the extracellular matrix (ECM). Therefore, deciphering their role in the biologically relevant context is important for fundamental understanding of the processes ongoing in ECM and for establishing new strategies in the regenerative medicine. Although GAGs represent a number of computational challenges, molecular docking is a powerful tool for analysis of their interactions. Despite the recent development of GAG-specific docking approaches, there is plenty of room for improvement...
March 25, 2021: Journal of Computational Chemistry
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