Journal of Computational Chemistry

Investigation of Lewis acid-base interactions has been conducted by ab initio calculations and machine learning (ML) models. This study aims to resolve two critical tasks that have not been quantitatively investigated. First, ML models developed from density functional theory (DFT) calculations predict experimental BF3 affinity with Pearson correlation coefficients around 0.9 and mean absolute errors around 10 kJ mol-1 . The ML models are trained by DFT-calculated BF3 affinity of more than 3000 adducts, with input features readily obtained by rdkit...

Inhibiting the enzymes carbonic anhydrase I (CA I) and carbonic anhydrase II (CA II) presents a potential avenue for addressing nervous system ailments such as glaucoma and Alzheimer's disease. Our study explored harnessing explainable artificial intelligence (XAI) to unveil the molecular traits inherent in CA I and CA II inhibitors. The PubChem molecular fingerprints of these inhibitors, sourced from the ChEMBL database, were subjected to detailed XAI analysis. The study encompassed training 10 regression models using IC50 values, and their efficacy was gauged using metrics including R2 , RMSE, and time taken...

An auxiliary polarization formulation of the fragment molecular orbital (FMO) method is developed, combining a basis set correction computed for capped isolated fragments with a polarization obtained from uncapped fragments. For a set of organic and inorganic test systems, it is shown that the total energy and atomic charges are accurately reproduced with respect to full unfragmented calculations. It is demonstrated that the method is accurate for computing electronic excited states. The developed approach is applied to rank the isomers of chignolin from experimental NMR data (PDB: 1UAO) according to their relative energy...

This study employs grand canonical Monte Carlo (GCMC) simulations to investigate the impact of functional group modifications (CH3 , OH, NH2 , and OLi) on the adsorption performance of CH4 /N2 on Ni-MOF-74. The results revealed that functional group modifications significantly increased the adsorption capacity of Ni-MOF-74 for both CH4 and N2 . The packed methyl groups in CH3 -Ni-MOF-74 create an environment conducive to CH4 , leading to the highest CH4 adsorption capacity...

The three-body recombination reaction, or ternary association, is a termolecular reaction leading to a molecule after a three-body encounter that plays a vital role in many relevant scenarios in chemical physics. Here, we introduce the Python 3-Body Recombination program, which is dedicated to the computation of atomic three-body recombination rate coefficients. The software is based on a classical trajectory approach in hyperspherical coordinates after mapping the three-body problem as a single particle in a higher-dimensional space...

Avena sativa phototropin 1 light-oxygen-voltage 2 domain (AsLOV2) is a model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N-terminal A'α helix in the dark state followed by the unfolding of the C-terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets are identified as crucial components for mediating allosteric signal transmission between the two termini...

Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D-RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D-RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker...

In a protein, nearby titratable sites can be coupled: the (de)protonation of one may affect the other. The degree of this interaction depends on several factors and can influence the measured <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"> <mml:semantics><mml:mrow><mml:mtext>p</mml:mtext> <mml:msub><mml:mrow><mml:mtext>K</mml:mtext></mml:mrow> <mml:mrow><mml:mtext>a</mml:mtext></mml:mrow> </mml:msub> </mml:mrow> <mml:annotation>$$ \mathrm{p}{K}_{\mathrm{a}} $$</mml:annotation></mml:semantics> </mml:math> ...

<mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"><mml:semantics><mml:mrow><mml:msub><mml:mi>B</mml:mi> <mml:mn>6</mml:mn></mml:msub> <mml:msub><mml:mi>O</mml:mi> <mml:mn>7</mml:mn></mml:msub> <mml:msubsup><mml:mfenced><mml:mi>OH</mml:mi></mml:mfenced> <mml:mn>6</mml:mn> <mml:mrow><mml:mn>2</mml:mn> <mml:mo>-</mml:mo></mml:mrow> </mml:msubsup> </mml:mrow> <mml:annotation>$$ {\mathrm{B}}_6{\mathrm{O}}_7{\left(\mathrm{OH}\right)}_6^{2-} $$</mml:annotation></mml:semantics> </mml:math> is a highly polymerized borate anion of three six-membered rings...

Thanks to recent developments in hardware and software, quantum chemical methods are increasingly used for interpreting the complex mechanisms underlying polymerization reaction by homogeneous catalysis. Unfortunately, the dimensions of even the smallest realistic models are too large to permit the use of state-of-the-art composite wave function methods. Under these circumstances, density functional theory still offers the best compromise between cost and accuracy. However, comprehensive benchmarks of different functionals are not yet available for this important research field...

In this article, density functional theory computations at the PBE0-D3/def2-TZVP level are reported to unveil the type of bonding between β-D-glucopyranose-silver ion (1:1) complex ([Ag(C6 H12 O6 )]+ ) and seven gas molecules, namely, H2 , C2 H2 , C2 H4 , CO, N2 , NO and O2 . Moreover, the relative preference of trapping among these molecules within the sight of Ag metal ion in the complex is explored. The nature of interaction of these small molecules with the [Ag(C6 H12 O6 )]+ ion is studied. Exergonic nature of binding is noted with the metal center for all the chosen small molecules except O2 ...

Determination of equilibrium molecular structures is an essential ingredient in predicting spectroscopic parameters that help in identifying molecular carriers of microwave transitions. Here, the performance of two different ab initio composite approaches for obtaining equilibrium structures, "energy scheme" and "geometry scheme," is explored and compared to semi-experimental equilibrium structures. This study is performed for a set of 11 molecules which includes diatomics, linear triatomics, and a few non-linear molecules...

Terthiophene derivatives attract interest due to their prospective applications in optoelectronic or sensor devices. Due to their nontoxicity they can be considered as suitable candidates in biological applications. Supramolecular organization of the matter is one of the most interesting topics in contemporary materials science. Amphiphilic chromophores based on substituted terthiophenes are capable of self-assembly into supramolecular architectures. In this work, we aim at simulation of the spectral properties of terthiophene with oligo(ethylene oxide) substituents by the methods of quantum chemistry and molecular dynamics (MD)...

For a detailed understanding of chemical processes in nature and industry, we need accurate models of chemical reactions in complex environments. While Eyring transition state theory is commonly used for modeling chemical reactions, it is most accurate for small molecules in the gas phase. A wide range of alternative rate theories exist that can better capture reactions involving complex molecules and environmental effects. However, they require that the chemical reaction is sampled by molecular dynamics simulations...

Electrical equivalent circuits are a widely applied tool with which electrical processes can be rationalized. There is a wide-ranging selection of fields from bioelectrochemistry to batteries to fuel cells making use of this tool. Enabling meta-analysis on the similarities and differences in the used circuits will help to identify commonly used circuits and aid in evaluating the underlying physics. We present a method and an implementation that enables the conversion of circuits included in scientific publications into a machine-readable form for generating machine learning datasets or circuit simulations...

Understanding interactions of inorganic nanoparticles with biomolecules is important in many biotechnology, nanomedicine, and toxicological research, however, the size of typical nanoparticles makes their direct modeling by atomistic simulations unfeasible. Here, we present a bottom-up coarse-graining approach for modeling titanium dioxide (TiO <mml:math xmlns:mml="https://www.w3.org/1998/Math/MathML"> <mml:semantics> <mml:mrow><mml:msub><mml:mrow/> <mml:mrow><mml:mn>2</mml:mn></mml:mrow> </mml:msub> </mml:mrow> <mml:annotation>$$ {}_2 $$</mml:annotation></mml:semantics> </mml:math> ) nanomaterials in contact with phospholipids that uses the inverse Monte Carlo method to optimize the effective interactions from the structural data obtained in small-scale all-atom simulations of TiO <mml:math xmlns:mml="https://www...

Vibrational spectroscopy enables critical insight into the structural and dynamic properties of molecules. Presently, the majority of theoretical approaches to spectroscopy employ wavefunction-based ab initio or density functional methods that rely on the harmonic approximation. This approximation breaks down for large molecules with strongly anharmonic bonds or for molecules with large internuclear separations. An alternative to these methods involves generating molecular anharmonic potential energy surfaces (potentials) and using them to extrapolate the vibrational frequencies...

In this study, the enantioselectivity of β-cyclodextrin and its derivatives towards propranolol enantiomers are investigated by molecular dynamic (MD) simulations. β-cyclodextrin (β-CD) have previously been shown to be able to recognize propranolol (PRP) enantiomers. To improve upon the enantioselectivity of β-cyclodextrin, we propose the use of an ionic-liquid-modified-β-cyclodextrin (β-CD-IL). β-CD-IL was found to be able to complex R and S propranolol enantiomers with differing binding energies...

This study addresses a comprehensive assessment of the interaction between chemical warfare agents (CWA) and acetylcholinesterase (AChE) systems, focus on the intriguing pnictogen-bond interaction (PnB). Utilizing the crystallographic data from the Protein Data Bank pertaining to the AChE-CWA complex involving Sarin (GB), Cyclosarin (GF), 2-[fluoro(methyl)phosphoryl]oxy-1,1-dimethylcyclopentane (GP) and venomous agent X (VX) agents, the CWA is systematically displaced by increments of 0.1 Å along the PO bond axis, extending its distance by 4 Å from the original position...

The modulation of the photophysical properties of di-substituted porphyrin rings upon the oxygen and sulfur-for-nitrogen replacement has been investigated at density functional theory (DFT) and its time-dependent formulation (TDDFT). The considered properties range from structural behaviors and excitation energies to spin-orbit coupling (SOC) and nonradiative intersystem kinetic constants. Results show that the SOC strongly increase upon chalcogen substitution and, accordingly, the computed nonradiative kinetic constant also indicate an efficient singlet-triplet intersystem crossing in the sulfur containing macrocycle...