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Research Articles

Online and desktop graphical user interfaces for xtb programme from atomistica.online platform

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Pages 560-570 | Received 18 Jan 2024, Accepted 07 Mar 2024, Published online: 19 Mar 2024

References

  • Neese F, Wennmohs F, Becker U, et al. The ORCA quantum chemistry program package. J Chem Phys. 2020;152:224108, doi:10.1063/5.0004608
  • Armaković S, Armaković SJ, Koziel S. Optoelectronic properties of curved carbon systems. Carbon N Y. 2017;111:371–379. doi:10.1016/j.carbon.2016.10.022
  • Bielenica A, Beegum S, Mary YS, et al. Experimental and computational analysis of 1-(4-chloro-3-nitrophenyl)−3-(3,4-dichlorophenyl)thiourea. J Mol Struct. 2020;1205:127587, doi:10.1016/j.molstruc.2019.127587
  • Armaković S, Armaković JS. Investigation of boron modified graphene nanostructures; optoelectronic properties of graphene nanoparticles and transport properties of graphene nanosheets. J Phys Chem Solids. 2016;98:156–166. doi:10.1016/j.jpcs.2016.07.006
  • Aneesh Kumar R, Jamelah Al-Otaibi S, Sheena Mary Y, et al. Surface adsorption of adenine on pristine and B/N/O/P-doped coronene as a biosensing substrate for DNA detection- DFT study. J Mol Liq. 2024: 123546, doi:10.1016/j.molliq.2023.123546
  • Al-Otaibi JS, Mary YS, Mary YS, et al. Evidences of noncovalent interactions between indole and dichloromethane under different solvent conditions. J Mol Model. 2023;29:246, doi:10.1007/s00894-023-05623-3
  • Afroz Bakht M, Alharthi AI, Thangaiyan P, et al. Interaction of serotonin and histamine with water and ethanol: evidence from theoretical investigations. Comput Theor Chem. 2023;1228:114299, doi:10.1016/j.comptc.2023.114299
  • Akpe MA, Okon GA, Louis H, et al. Metals (Ga, In) decorated fullerenes as nanosensors for the adsorption of 2,2-dichlorovinyldimethylphosphate agrochemical based pollutant. Sci Rep. 2023;13:10470, doi:10.1038/s41598-023-37650-8
  • Mary YS, Mary YS, Thomas R, et al. Theoretical studies on the structure and various physico-chemical and biological properties of a terphenyl derivative with immense anti-protozoan activity. Polycycl Aromat Compd. 2021;41:825–840. doi:10.1080/10406638.2019.1624974
  • Thiel W. Semiempirical quantum–chemical methods. WIREs Comput Mol Sci. 2014;4:145–157. doi:10.1002/wcms.1161
  • Stokbro K, Petersen DE, Smidstrup S, et al. Semiempirical model for nanoscale device simulations. Phys Rev B. 2010;82:075420, doi:10.1103/PhysRevB.82.075420
  • Stewart JJP. Optimization of parameters for semiempirical methods II. Applications. J Comput Chem. 1989;10:221–264. doi:10.1002/jcc.540100209
  • Stewart JJP. Optimization of parameters for semiempirical methods I. Method. J Comput Chem. 1989;10:209–220. doi:10.1002/jcc.540100208
  • Stewart JJP. Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. J Mol Model. 2007;13:1173–1213. doi:10.1007/s00894-007-0233-4
  • Stewart JJP. Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters. J Mol Model. 2013;19:1–32. doi:10.1007/s00894-012-1667-x
  • Orozco M, Bachs M, Luque FJ. Development of optimized MST/SCRF methods for semiempirical calculations: the MNDO and PM3 Hamiltonians. J Comput Chem. 1995;16:563–575. doi:10.1002/jcc.540160505
  • Suitability of the PM3-derived molecular electrostatic potentials - Alemán - 1993 - Journal of Computational Chemistry - Wiley Online Library, (n.d.). https://onlinelibrary.wiley.com/doi/abs/10.1002jcc.540140706 (accessed March 3, 2024).
  • Köhler C, Seifert G, Frauenheim T. Density functional based calculations for Fen (n≤32). Chem Phys. 2005;309:23–31. doi:10.1016/j.chemphys.2004.03.034
  • Seifert G, Porezag D, Frauenheim T. Calculations of molecules, clusters, and solids with a simplified LCAO-DFT-LDA scheme. Int J Quantum Chem. 1996;58:185–192. doi:10.1002/(SICI)1097-461X(1996)58:2<185::AID-QUA7>3.0.CO;2-U
  • Elstner M, Porezag D, Jungnickel G, et al. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Phys Rev B. 1998;58:7260–7268. doi:10.1103/PhysRevB.58.7260
  • Porezag D, Frauenheim T, Köhler T, et al. Construction of tight-binding-like potentials on the basis of density-functional theory: application to carbon. Phys Rev B. 1995;51:12947–12957. doi:10.1103/PhysRevB.51.12947
  • Niehaus TA, Suhai S, Sala FD, et al. Tight-binding approach to time-dependent density-functional response theory. Phys Rev B. 2001;63:085108, doi:10.1103/PhysRevB.63.085108
  • Bannwarth C, Caldeweyher E, Ehlert S, et al. Extended tight-binding quantum chemistry methods. WIRES Comput Mol Sci. 2021;11:e1493, doi:10.1002/wcms.1493
  • Bannwarth C, Ehlert S, Grimme S. GFN2-xTB-An accurate and broadly parametrized self-consistent tight-binding quantum chemical method with multipole electrostatics and density-dependent dispersion contributions. J Chem Theory Comput. 2019;15:1652–1671. doi:10.1021/acs.jctc.8b01176
  • Ehlert S, Stahn M, Spicher S, et al. Robust and efficient implicit solvation model for fast semiempirical methods. J Chem Theory Comput. 2021;17:4250–4261. doi:10.1021/acs.jctc.1c00471
  • Pracht P, Caldeweyher E, Ehlert S, et al. A robust non-self-consistent tight-binding quantum chemistry method for large molecules, (2019). doi:10.26434/chemrxiv.8326202.v1.
  • Grimme S, Bannwarth C, Shushkov P. A robust and accurate tight-binding quantum chemical method for structures, vibrational frequencies, and noncovalent interactions of large molecular systems parametrized for All spd-block elements (Z= 1–86). J Chem Theory Comput. 2017;13:1989–2009. doi:10.1021/acs.jctc.7b00118
  • Schrödinger - Physics-based Software Platform for Molecular Discovery & Design. Schrödinger (n.d.). https://newsite.schrodinger.com/ (accessed January 16, 2024).
  • Amsterdam modeling suite making computational chemistry work For You. Software for Chemistry & Materials (n.d.). https://www.scm.com/ (accessed January 16, 2024).
  • Anvil: Web Apps with Nothing but Python. Anvil (n.d.). https://anvil.works/ (accessed January 16, 2024).
  • Armaković S, Armaković JS. Atomistica.online – web application for generating input files for ORCA molecular modelling package made with the Anvil platform. Mol Simul. 2023;49:117–123. doi:10.1080/08927022.2022.2126865
  • Spicher S, Grimme S. Robust atomistic modeling of materials, organometallic, and biochemical systems. Angew Chem Int Ed. 2020;59:15665–15673. doi:10.1002/anie.202004239
  • Caldeweyher E, Ehlert S, Hansen A, et al. A generally applicable atomic-charge dependent London dispersion correction. J Chem Phys. 2019;150:154122, doi:10.1063/1.5090222
  • Koopman J, Grimme S. Calculation of mass spectra with the QCxMS method for negatively and multiply charged molecules, (2022). doi:10.26434/chemrxiv-2022-w5260.
  • Schnegotzki R, Koopman J, Grimme S, et al. Quantum chemistry-based molecular dynamics simulations as a tool for the assignment of ESI-MS/MS spectra of drug molecules. Chem Eur J. 2022;28:e202200318, doi:10.1002/chem.202200318
  • Schreckenbach SA, Anderson JSM, Koopman J, et al. Predicting the mass spectra of environmental pollutants using computational chemistry: a case study and critical evaluation. J Am Soc Mass Spectrom. 2021;32:1508–1518. doi:10.1021/jasms.1c00078
  • Koopman J, Grimme S. From QCEIMS to QCxMS: a tool to routinely calculate CID mass spectra using molecular dynamics. J Am Soc Mass Spectrom. 2021;32:1735–1751. doi:10.1021/jasms.1c00098
  • Ásgeirsson V, Bauer CA, Grimme S. Unimolecular decomposition pathways of negatively charged nitriles by ab initio molecular dynamics. Chem Chem Phys. 2016;18:31017–31026. doi:10.1039/C6CP06180J
  • Koopman J, Grimme S. Calculation of electron ionization mass spectra with semiempirical GFNn-xTB methods. ACS Omega. 2019;4:15120–15133. doi:10.1021/acsomega.9b02011
  • Ásgeirsson V, Bauer CA, Grimme S. Quantum chemical calculation of electron ionization mass spectra for general organic and inorganic molecules. Sci. 2017;8:4879–4895. doi:10.1039/C7SC00601B
  • Bauer CA, Grimme S. How to compute electron ionization mass spectra from first principles. J Phys Chem A. 2016;120:3755–3766. doi:10.1021/acs.jpca.6b02907
  • Bauer CA, Grimme S. Automated quantum chemistry based molecular dynamics simulations of electron ionization induced fragmentations of the nucleobases uracil, thymine, cytosine, and guanine. Eur J Mass Spectrom (Chichester). 2015;21:125–140. doi:10.1255/ejms.1313
  • Bauer CA, Grimme S. Elucidation of electron ionization induced fragmentations of adenine by semiempirical and density functional molecular dynamics. J Phys Chem A. 2014;118:11479–11484. doi:10.1021/jp5096618
  • Bauer CA, Grimme S. First principles calculation of electron ionization mass spectra for selected organic drug molecules. Biomol Chem. 2014;12:8737–8744. doi:10.1039/C4OB01668H
  • Grimme S. Towards first principles calculation of electron impact mass spectra of molecules. Angew Chem Int Ed. 2013;52:6306–6312. doi:10.1002/anie.201300158
  • Hehre WJ, Stewart RF, Pople JA. Self-Consistent molecular-orbital methods. I. Use of Gaussian expansions of slater-type atomic orbitals. J Chem Phys. 1969;51:2657–2664. doi:10.1063/1.1672392
  • TIOBE Index. (n.d.). https://www.tiobe.com/tiobe-index/ (accessed June 1, 2022).
  • PYPL Index. (n.d.). https://pypl.github.io/PYPL.html (accessed June 1, 2022).
  • Python Software Foundation. Python Language Reference, version 3.11 Available at http://www.python.org, (n.d.).
  • Van Rossum G, Drake FL. Python tutorial. The Netherlands: Centrum voor wiskunde en informatica Amsterdam; 1995.
  • Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/, (n.d.).

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