Browsing by Subject "AB-INITIO"

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  • Lehtola, Susi; Blockhuys, Frank; Van Alsenoy, Christian (2020)
    A uniform derivation of the self-consistent field equations in a finite basis set is presented. Both restricted and unrestricted Hartree-Fock (HF) theory as well as various density functional approximations are considered. The unitary invariance of the HF and density functional models is discussed, paving the way for the use of localized molecular orbitals. The self-consistent field equations are derived in a non-orthogonal basis set, and their solution is discussed also in the presence of linear dependencies in the basis. It is argued why iterative diagonalization of the Kohn-Sham-Fock matrix leads to the minimization of the total energy. Alternative methods for the solution of the self-consistent field equations via direct minimization as well as stability analysis are briefly discussed. Explicit expressions are given for the contributions to the Kohn-Sham-Fock matrix up to meta-GGA functionals. Range-separated hybrids and non-local correlation functionals are summarily reviewed.
  • Shao, Yihan; Mei, Ye; Sundholm, Dage; Kaila, Ville R. I. (2020)
    Quantum chemical calculations are important for elucidating light-capturing mechanisms in photobiological systems. The time-dependent density functional theory (TDDFT) has become a popular methodology because of its balance between accuracy and computational scaling, despite its problems in describing, for example, charge transfer states. As a step toward systematically understanding the performance of TDDFT calculations on biomolecular systems, we study here 17 commonly used density functionals, including seven long-range separated functionals, and compare the obtained results with excitation energies calculated at the approximate second order coupled-cluster theory level (CC2). The benchmarking set includes the first five singlet excited states of 11 chemical analogues of biochromophores from the green fluorescent protein, rhodopsin/bacteriorhodopsin (Rh/bR), and the photoactive yellow protein. We find that commonly used pure density functionals such as BP86, PBE, M11-L, and hybrid functionals with 20-25% of Hartree-Fock (HF) exchange (B3LYP, PBE0) have a tendency to consistently underestimate vertical excitation energies (VEEs) relative to the CC2 values, whereas hybrid density functionals with around 50% HF exchange such as BHLYP, PBE50, and M06-2X and long-range corrected functionals such as CAM-B3LYP, omega PBE, omega PBEh, omega B97X, omega B97XD, BNL, and M11 overestimate the VEEs. We observe that calculations using the CAM-B3LYP and omega PBEh functionals with 65% and 100% long-range HF exchange, respectively, lead to an overestimation of the VEEs by 0.2-0.3 eV for the benchmarking set. To reduce the systematic error, we introduce here two new empirical functionals, CAMh-B3LYP and omega hPBE0, for which we adjusted the long-range HF exchange to 50%. The introduced parameterization reduces the mean signed average (MSA) deviation to 0.07 eV and the root mean square (rms) deviation to 0.17 eV as compared to the CC2 values. In the present study, TDDFT calculations using the aug-def2-TZVP basis sets, the best performing functionals relative to CC2 are omega hPBE0 (rms = 0.17, MSA = 0.06 eV); CAMh-B3LYP (rms = 0.16, MSA = 0.07 eV); and PBE0 (rms = 0.23, MSA = 0.14 eV). For the popular range-separated CAM-B3LYP functional, we obtain an rms value of 0.31 eV and an MSA value of 0.25 eV, which can be compared with the rms and MSA values of 0.37 and -0.31 eV, respectively, as obtained at the B3LYP level.
  • Franzke, Yannick J.; Sundholm, Dage; Weigendb, Florian (2017)
    Magnetically induced current density susceptibilities have been studied for a number of cyclic ethyne and butadiyne-bridged porphyrin and isoporphyrin arrays. The current density susceptibilities have been calculated using the gauge-including magnetically induced current (GIMIC) method, which is interfaced to the TURBOMOLE quantum chemistry code. Aromatic properties and current pathways have been analyzed and discussed by numerical integration of the current density susceptibilities passing selected chemical bonds yielding current strength susceptibilities. Despite the interrupted p-framework, zinc(II) isoporphyrin sustains a ring current of ca. 10 nA T-1. Porphyrin and isoporphyrin dimers sustain a significant current strength at the linker, whereas the larger porphyrinoid arrays sustain mainly local ring currents. Isoporphyrin dimers with saturated meso carbons have strong net diatropic ring-current strengths of 20 nA T-1 fulfilling Huckels aromaticity rule. Porphyrin trimers and tetramers exhibit almost no current strength at the linker. The porphyrin moieties maintain their strong net diatropic ring current.
  • Keshavarz, Fatemeh; Shcherbacheva, Anna; Kubecka, Jakub; Vehkamäki, Hanna; Kurten, Theo (2019)
    The effect of dust aerosols on accretion reactions of water, formaldehyde, and formic acid was studied in the conditions of earth's troposphere at the DLPNO-CCSD(T)/aug-cc-pVTZ//omega B97X-D/6-31++G** level of theory. A detailed analysis of the reaction mechanisms in the gas phase and on the surface of mineral dust, represented by mono- and trisilicic acid, revealed that mineral dust has the potential of decreasing reaction barrier heights. Specifically, at 0 K, mineral dust can lower the apparent energy barrier of the reaction of formaldehyde with formic acid to zero. However, when the entropic contributions to the reaction free energies were accounted for, mineral dust was found to selectively enhance the reaction of water with formaldehyde, while inhibiting the reaction of formaldehyde and formic acid, in the lower parts of the troposphere (with temperatures around 298 K). In the upper troposphere (with temperatures closer to 198 K), mineral dust catalyzes both reactions and also the reaction of methanol with formic acid. Despite the intrinsic potential of mineral dust, calculation of the catalytic enhancement parameter for a likely range of dust aerosol concentrations suggested that dust aerosols will not contribute to secondary organic aerosol formation via dimerization of closed-shell organic compounds. The main reason for this is the relatively low absolute concentratign of tropospheric dust aerosol and its inefficiency in increasing the effective reaction rate coefficients.
  • Rasmussen, Freja Rydahl; Kubecka, Jakub; Besel, Vitus; Vehkamäki, Hanna; Mikkelsen, Kurt V.; Bilde, Merete; Elm, Jonas (2020)
    Sampling the shallow free energy surface of hydrated atmospheric molecular clusters is a significant challenge. Using computational methods, we present an efficient approach to obtain minimum free energy structures for large hydrated clusters of atmospheric relevance. We study clusters consisting of two to four sulfuric acid (sa) molecules and hydrate them with up to five water (w) molecules. The structures of the "dry" clusters are obtained using the ABCluster program to yield a large pool of low-lying conformer minima with respect to free energy. The conformers (up to ten) lowest in free energy are then hydrated using our recently developed systematic hydrate sampling technique. Using this approach, we identify a total of 1145 unique (sa)(2-4)(w)(1-5) cluster structures. The cluster geometries and thermochemical parameters are calculated at the omega B97X-D/6-31++G(d,p) level of theory, at 298.15 K and 1 atm. The single-point energy of the most stable clusters is calculated using a high-level DLPNO-CCSD(T-0)/aug-cc-pVTZ method. Using the thermochemical data, we calculate the equilibrium hydrate distribution of the clusters under atmospheric conditions and find that the larger (sa)(3) and (sa)(4) clusters are significantly more hydrated than the smaller (sa)(2) cluster or the sulfuric acid (sa)(1) molecule. These findings indicate that more than five water molecules might be required to fully saturate the sulfuric acid clusters with water under atmospheric conditions. The presented methodology gives modelers a tool to take the effect of water explicitly into account in atmospheric particle formation models based on quantum chemistry.
  • Johansson, Mikael P.; Swart, Marcel (2013)
    By analysing the properties of the electron density in the structurally simple perhalogenated ethanes, X3C–CY3 (X, Y = F, Cl), a previously overlooked non-covalent attraction between halogens attached to opposite carbon atoms is found. Quantum chemical calculations extrapolated towards the full solution of the Schrödinger equation reveal the complex nature of the interaction. When at least one of the halogens is a chlorine, the strength of the interaction is comparable to that of hydrogen bonds. Further analysis shows that the bond character is quite different from standard non-covalent halogen bonds and hydrogen bonds; no bond critical points are found between the halogens, and the σ-holes of the halogens are not utilised for bonding. Thus, the nature of the intramolecular halogen···halogen bonding studied here appears to be of an unusually strong van der Waals type.
  • Willmann, Knut; Vent-Schmidt, Thomas; Rasanen, Markku; Riedel, Sebastian; Khriachtchev, Leonid (2015)
    The HKrCCH center dot center dot center dot HCCH complex is identified in a Kr matrix with the H-Kr stretching bands at 1316.5 and 1305 cm(-1). The monomer-to-complex shift of the H-Kr stretching mode is about +60 cm(-1), which is significantly larger than that reported previously for the HXeCCH center dot center dot center dot HCCH complex in a Xe matrix (about +25 cm(-1)). The HKrCCH center dot center dot center dot HCCH complex in a Kr matrix is formed at similar to 40 K via the attachment of mobile acetylene molecules to the HKrCCH monomers formed at somewhat lower annealing temperatures upon thermally-induced mobility of H atoms (similar to 30 K). The same mechanism was previously proposed for the formation of the HXeCCH center dot center dot center dot HCCH complex in a Xe matrix. The assignment of the HKrCCH center dot center dot center dot HCCH complex is fully supported by the quantum chemical calculations. The experimental shift of the H-Kr stretching mode is comparable with the computational predictions (+46.6, +66.0, and +83.2 cm(-1) at the B3LYP, MP2, and CCSD(T) levels of theory, respectively), which are also bigger that the calculated shift in the HXeCCH center dot center dot center dot HCCH complex. These results confirm that the complexation effect is bigger for less stable noble-gas hydrides.
  • Sundholm, Dage; Rauhalahti, Markus; Özcan, Nergiz; Mera-Adasme, Raul; Kussmann, Jorg; Luenser, Arne; Ochsenfeld, Christian (2017)
    Nuclear magnetic shieldings have been calculated at the density functional theory (DFT) level for stacks of benzene, hexadehydro[12]annulene, dodecadehydro[18]annulene, and hexabenzocoronene. The magnetic shieldings due to the ring currents in the adjacent molecules have been estimated by calculating nucleus independent molecular shieldings for the monomer in the atomic positions of neighbor molecules. The calculations show that the independent shielding model works reasonably well for the H-1 NMR shieldings of benzene and hexadehydro[12]annulene, whereas for the larger molecules and for the C-13 NMR shieldings the interaction between the molecules leads to shielding effects that are at least of the same size as the ring current contributions from the adjacent molecules. A better agreement is obtained when the nearest neighbors are also considered at full quantum mechanical (QM) level. The calculations suggest that the nearest solvent molecules must be included in the quantum mechanical system, at least when estimating solvent shifts at the molecular mechanics (MM) level. Current density calculations show that the stacking does not significantly affect the ring current strengths of the individual molecules, whereas the shape of the ring current for a single molecule differs from that of the stacked molecules.
  • Castin, N.; Bakaev, A.; Bonny, G.; Sand, A. E.; Malerba, L.; Terentyev, D. (2017)
    We propose an object kinetic Monte Carlo (OKMC) model for describing the microstructural evolution in pure tungsten under neutron irradiation. We here focus on low doses ( under 1 dpa), and we neglect transmutation in first approximation. The emphasis is mainly centred on an adequate description of neutron irradiation, the subsequent introduction of primary defects, and their thermal diffusion properties. Besides grain boundaries and the dislocation network, our model includes the contribution of carbon impurities, which are shown to have a strong influence on the onset of void swelling. Our parametric study analyses the quality of our model in detail, and confronts its predictions with experimental microstructural observations with satisfactory agreement. We highlight the importance for an accurate determination of the dissolved carbon content in the tungsten matrix, and we advocate for an accurate description of atomic collision cascades, in light of the sensitivity of our results with respect to correlated recombination. (C) 2017 Published by Elsevier B.V.
  • John, Jerin Susan; Sajan, D.; Narayana, Chandrabhas; Sundius, T. (2018)
    The search for a potential nonlinear optical (NLO) material has led to the investigation of an organic compound 4-[(E)-2-(2,4,6-Trinitrophenyl)ethylidene]benzonitrile (TEB), which has a possibility of enhancing the NLO properties by the charge transfer mechanism if metal atoms are adsorbed on it. The experimental characterization of TEB is done using Fourier Transform Infrared (FT-IR), Fr-Raman, Ultraviolet-visible (UV-Visible), Photoluminescence (PL), Thermogravimetric/Differential Thermal Analysis (TG/DTA) and Z-scan techniques. The third order NLO properties evaluated using Z-scan technique proves that the material can be used as a good optical limiter. TEB is attached with silver atoms and the theoretical studies including geometry optimization, NBO analysis and hyperpolarizability calculations are carried out. The TEB molecule with silver atoms adsorbed is found to have increased hyperpolarizability values. The charge transfer from the metal atom to the nitrile group of the molecule is evident from the Surface Enhanced Raman Scattering (SERS) spectra using the silver nanoparticles. (C) 2018 Elsevier Ltd. All rights reserved.
  • Elm, Jonas; Myllys, Nanna; Kurten, Theo (2017)
    We investigate the molecular interactions between phosphoric acid and common atmospheric nucleation precursors using computational methods. The equilibrium geometries and vibrational frequencies are obtained using the three DFT functionals M06-2X, PW91 and B97X-D. The single-point energy is corrected using a high-level CCSD(T)-F12a/VDZ-F12 calculation. The molecular interaction between phosphoric acid and sulphuric acid is found to be strong with reaction free energy of similar magnitude as the interaction between dimethylamine and sulphuric acid. The strong hydrogen bonding of phosphoric acid to sulphuric acid indicates that concentrations of as low as 10(2)-10(4) molecules/cm(3) will offer equivalent or higher stability as the sulphuric acid dimer for the formation of atmospheric molecular clusters. We assess and utilise the DLPNO-CCSD(T) method for studying larger clusters involving phosphoric acid and sulphuric acid and find that having a phosphoric acid molecule present in the cluster enhances the further addition of sulphuric acid molecules. [GRAPHICS] .
  • Valiev, R. R.; Berezhnoy, A. A.; Gritsenko, I. S.; Merzlikin, B. S.; Cherepanov, Viktor N.; Kurten, Theo; Wöhler, Chrisitan (2020)
    We calculated the cross sections of photolysis of OH, LiO, NaO, KO, HCl, LiCl, NaCl, KCl, HF, LiF, NaF, and KF molecules using quantum chemistry methods. The maximal values for photolysis cross sections of alkali metal monoxides are on the order of 10(-18) cm(2). The lifetimes of photolysis for quiet Sun at 1 astronomical unit are estimated as 2.0 x 10(5), 28, 5, 14, 2.1 x 10(5), 225, 42, 52, 2 x 10(6), 35 400, 486, and 30 400 s for OH, LiO, NaO, KO, HCl, LiCl, NaCl, KCl, HF, LiF, NaF, and KF, respectively. We performed a comparison between values of photolysis lifetimes obtained in this work and in previous studies. Based on such a comparison, our estimations of photolysis lifetimes of OH, HCl, and HF have an accuracy of about a factor of 2. We determined typical kinetic energies of main peaks of photolysis-generated metal atoms. Impact-produced LiO, NaO, KO, NaCl, and KCl molecules are destroyed in the lunar and Hermean exospheres almost completely during the first ballistic flight, while other considered molecules are more stable against destruction by photolysis.
  • Sundholm, Dage; Rabaa, Hassan; Chiheb, Mohammed; Balch, Alan L. (2019)
    Calculations have been performed at the MP2 and DFT levels for investigating the reasons for the difficulties in synthesizing bis(isocyanide)gold(I) halide complexes. Three-coordinated gold(I) complexes of the type (R3P)(2)(AuX)-X-I (1) can be synthesized, whereas the analogous isocyanide complexes (RNC)(2)(AuX)-X-I (2) are not experimentally known. The molecular structures of (R3P)(2)(AuX)-X-I (X = Cl, Br, and I) and (RNC)(2)(AuX)-X-I with X = halide, cyanide, nitrite, methylthiolate, and thiocyanate are compared and structural differences are discussed. Calculations of molecular properties elucidate which factors determine the strength of the gold-ligand interactions in (RNC)(2)(AuX)-X-I. The linear bonding mode of RNC favors a T-shaped geometry instead of the planar Y-shaped trigonal structure of (R3P)(2)(AuX)-X-I complexes that have been synthesized. An increased polarity of the Au-X bond in 2 leads to destabilization of the Y-shaped structure. Chalcogen-containing ligands or cyanide appear to be good X-ligand candidates for synthesis of (RNC)(2)(AuX)-X-I complexes.
  • Sun, Qiming; Zhang, Xing; Banerjee, Samragni; Bao, Peng; Barbry, Marc; Blunt, Nick S.; Bogdanov, Nikolay A.; Booth, George H.; Chen, Jia; Cui, Zhi-Hao; Eriksen, Janus Juul; Gao, Yang; Guo, Sheng; Hermann, Jan; Hermes, Matthew R.; Koh, Kevin; Koval, Peter; Lehtola, Susi; Li, Zhendong; Liu, Junzi; Mardirossian, Narbe; McClain, James D.; Motta, Mario; Mussard, Bastien; Pham, Hung Q.; Pulkin, Artem; Purwanto, Wirawan; Robinson, Paul J.; Ronca, Enrico; Sayfutyarova, Elvira; Scheurer, Maximilian; Schurkus, Henry F.; Smith, James E. T.; Sun, Chong; Sun, Shi-Ning; Upadhyay, Shiv; Wagner, Lucas K.; Wang, Xiao; White, Alec; Whitfield, James Daniel; Williamson, Mark J.; Wouters, Sebastian; Yang, Jun; Yu, Jason M.; Zhu, Tianyu; Berkelbach, Timothy C.; Sharma, Sandeep; Sokolov, Alexander; Chan, Garnet Kin-Lic (2020)
    PySCF is a Python-based general-purpose electronic structure platform that supports first-principles simulations of molecules and solids as well as accelerates the development of new methodology and complex computational workflows. This paper explains the design and philosophy behind PySCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PySCF as a development environment. We then summarize the capabilities of PySCF for molecular and solid-state simulations. Finally, we describe the growing ecosystem of projects that use PySCF across the domains of quantum chemistry, materials science, machine learning, and quantum information science. Published under license by AIP Publishing.
  • Li, Hao; Zhong, Jie; Vehkamäki, Hanna; Kurtén, Theo; Wang, Weigang; Ge, Maofa; Zhang, Shaowen; Li, Zesheng; Zhang, Xiuhui; Francisco, Joseph S.; Zeng, Xiao Cheng (2018)
    Sulfur trioxide (SO3) is one of the most active chemical species in the atmosphere, and its atmospheric fate has profound implications to air quality and human health. The dominant gas-phase loss pathway for SO3 is generally believed to be the reaction with water molecules, resulting in sulfuric acid. The latter is viewed as a critical component in the new particle formation (NPF). Herein, a new and competitive loss pathway for SO3 in the presence of abundant gas-phase ammonia (NH3) species is identified. Specifically, the reaction between SO3 and NH3, which produces sulfamic acid, can be self-catalyzed by the reactant (NH3). In dry and heavily polluted areas with relatively high concentrations of NH3, the effective rate constant for the bimolecular SO3-NH3 reaction can be sufficiently fast through this new loss pathway for SO3 to become competitive with the conventional loss pathway for SO3 with water. Furthermore, this study shows that the final product of the reaction, namely, sulfamic acid, can enhance the fastest possible rate of NPF from sulfuric acid and dimethylamine (DMA) by about a factor of 2. An alternative source of stabilizer for acid-base clustering in the atmosphere is suggested, and this new mechanism for NPF has potential to improve atmospheric modeling in highly polluted regions.
  • Krachko, Tetiana; Ehlers, Andreas W.; Nieger, Martin; Lutz, Martin; Slootweg, J. Chris (2018)
    The phosphorus analogues of cyclopentadienone, tricyclopentanone, and housene were accessed from bis(cyclopropenyl)diphosphetanedione 3, which was prepared by mixing 1,2,3-tris-tert-butylcyclopropenium tetrafluoroborate (1) and sodium phosphaethynolate [Na(OCP)(dioxane)(n)]. While photolysis of 3 results in decarbonylation, yielding bis(cyclopropenyl)diphosphene 4 and after rearrangement diphosphahousene 5, thermolysis of 3 leads to phosphatricyclo[]pentanone 7. Metal-mediated valence isomerization of 7 and subsequent demetalation provides access to phosphacyclopentadienone 12.
  • Schwerdtfeger, Peter; Smits, Odile R.; Pyykkö, Pekka (2020)
    As the International Year of the Periodic Table came to an end in 2019, the authors reflect on the chemistry and physics that drive the periodic table of the elements. This includes aspects of periodic trends, relativistic electronic-structure theory, nuclear-structure theory and the astrophysical origin of the elements. Mendeleev's introduction of the periodic table of elements is one of the most important milestones in the history of chemistry, as it brought order into the known chemical and physical behaviour of the elements. The periodic table can be seen as parallel to the Standard Model in particle physics, in which the elementary particles known today can be ordered according to their intrinsic properties. The underlying fundamental theory to describe the interactions between particles comes from quantum theory or, more specifically, from quantum field theory and its inherent symmetries. In the periodic table, the elements are placed into a certain period and group based on electronic configurations that originate from the Pauli and Aufbau principles for the electrons surrounding a positively charged nucleus. This order enables us to approximately predict the chemical and physical properties of elements. Apparent anomalies can arise from relativistic effects, partial-screening phenomena (of type lanthanide contraction) and the compact size of the first shell of everyl-value. Further, ambiguities in electron configurations and the breakdown of assigning a dominant configuration, owing to configuration mixing and dense spectra for the heaviest elements in the periodic table. For the short-lived transactinides, the nuclear stability becomes an important factor in chemical studies. Nuclear stability, decay rates, spectra and reaction cross sections are also important for predicting the astrophysical origin of the elements, including the production of the heavy elements beyond iron in supernova explosions or neutron-star mergers. In this Perspective, we critically analyse the periodic table of elements and the current status of theoretical predictions and origins for the heaviest elements, which combine both quantum chemistry and physics.
  • Ryazantsev, Sergey V.; Duarte, Luis; Feldman, Vladimir I.; Khryachtchev, Leonid (2017)
    Vacuum ultraviolet (VUV, 130-170 nm) photochemistry of the H2O center dot center dot center dot CO complex is studied by matrix-isolation infrared spectroscopy. The H2O center dot center dot center dot CO complexes in Ne, Ar, Kr, and Xe matrices are generated by ultraviolet (UV, 193 and 250 nm) photolysis of formic acid (HCOOH). VUV photolysis of the H2O center dot center dot center dot CO complexes is found to lead to the formation of the OH center dot center dot center dot CO radical-molecule complexes and trans-HOCO radicals. It is shown that the matrix material, local matrix morphology, and possibly the H2O center dot center dot center dot CO complex geometry strongly affect the VUV photolysis pathways. The intrinsic reactivity of the matrix-isolated OH center dot center dot center dot CO complex resulting in the formation of trans-HOCO is directly demonstrated for the first time. This reaction occurs in Ar, Kr, and Xe matrices upon annealing above 25 K and may proceed over the barrier. The case of a Ne matrix is very special because the formation of trans-HOCO from the OH center dot center dot center dot CO complex is observed even at the lowest experimental temperature (4.5 K), which is in sharp contrast to the other matrices. It follows that quantum tunneling is probably involved in this process in the Ne matrix at such a low temperature. Infrared light also promotes this reaction in the Ne matrix at 4.5 K, which is not the case in the other matrices. The last findings show the effect of the environment on the tunneling and infrared-induced rates of this fundamental chemical reaction.