Density Functional Thermochemistry Research Articles

In situ mass spectrometric investigation to probe GeSn growth dynamics and mechanisms in the chemical vapor deposition processes

GeSn has attracted increasing attention due to its tunable bandgap from indirect to direct resulting in unique electronic and optoelectronic capabilities. Chemical vapor deposition (CVD) is well acknowledged as an advanced growth method for GeSn, demonstrating its capability with grown materials for infrared lasers and detector development. As an in situ diagnostics of the CVD process, a residual gas analyzer (RGA) could enable the detection of all gaseous species during growth, thus probing the growth dynamics and mechanism. Therefore, it is highly desirable but is lacking in the (Si)GeSn research community. This work utilized an RGA equipped with a specialized differential vacuum pumping system to analyze the mass spectra of the GeSn CVD precursors of SnCl4, GeH4, and their combination. The spectra of SnCl4 collected from gas samples at a standard base pressure of 0.3 Torr display consistent fragments with central mass-to-charge ratios (m/z) of 78, 120, 155, 225, and 260, corresponding to Sn+, SnCl2+, SnCl+, SnCl2+, SnCl3+, and SnCl4+, respectively. These profiles closely resemble those observed in the National Institute of Standards and Technology and Wiley and Matsumoto et al. The simultaneous introduction of SnCl4 and GeH4 at a combined pressure of several tens of Torr yields spectra, indicating a chemical reaction that produces GeCl4 at room temperature in the vacuum chamber and tubing. Utilizing Gaussian16 and ORCA codes, the ab initio and density functional thermochemistry computations were employed to predict potential essential reactions and validate the experimental findings.

Theoretical Study of the Formation Methane in the Reaction of Methyl Radical with Propanol-2

Theoretical Study of the Formation Methane in the Reaction of Methyl Radical with Propanol-2

How do you write and present research well? 17—Submit your manuscript to the journal you cite most

Abstract More people have cited Axel Becke's article on Density Functional Thermochemistry[1] than any other article between 1989 and 2014—over 45 000. How many citations has WoS indexed for the most cited chemical engineering paper?[2,3] less than 1000 between 1000 and 5000 between 5000 and 10 000 more than 10 000

Structural and Electronic Properties of Carbon-Nanotube/Graphene Junction: A First-Principles Study

Recently, a junction made of single wall carbon nanotube and a single sheet of graphene has been fabricated on silicon oxide substrate [1]. Their Raman spectroscopy measurements showed an upshift of the radial breathing modes and G peaks of the nanotube attributed to the charge transfer (CT) at the junction. The direction of the CT was determined from the intensity ratio of 2D/G of graphene, decreasing as a function of G Raman shift, which suggest n-doping of graphene due to the presence of nanotube. Their theoretical work, using molecular dynamics simulation, ruled out the strain on carbon nanotube to be the cause of the Raman upshift. In this work, we perform density functional theory calculations, for a model of C(13,7)/graphene junction, as suggested in Ref. [1]. Figure-1 shows the adopted model with 1132 carbon atoms, rendering the conventional first-principles methods that scale as O(N3) impractical. Therefore, we carried out the optimization of the large model using self-consistent density functional tight-binding method (SCC-DFTB), provided within CP2K package [2]. The resulting structure was then used to perform a single point energy calculation within density functional theory (DFT), adopting B97-D functional [3, 4], suitable for non-covalent interactions. The DFT is based on QUICKSTEP [5], which is an order-N method implemented in CP2K. Our preliminary results indicate that the charge transfer for a suspended nanotube/graphene system takes place from graphene to the carbon nanotube. To ascertain these results, we built a small material model consisting of the armchair C(10,10) and graphene junction, and performed calculations with the VASP package using optPBE [6] functional, which also includes the dispersion to account for van der Waals interactions. The results for the small model suggest an n-doping of carbon nanotube. Our findings are in agreement with the work of Cook et al. [7] for a C(8,0) adsorbed on a flat graphene junction. As can be seen, all the theoretical work seem to be in disagreement with the charge transfer direction, suggested in Ref. [1], which may be due to the pristine nature of the models. In this paper we will report on structural and electronic properties of a CNT/graphene junction, for pristine models as well as doped systems with impurities, where charge re-distribution at the junction will be outlined.1. Geraldine L. C. Paulus, et al., Charge Transfer at Junctions of a Single Layer of Graphene and a Metallic Single Walled Carbon Nanotube. Small, 2013. 9: p. 1954.2. CP2K. Available from: http://www.cp2k.org.3. Grimme, S., Semiemperical GGA-type density functional constructed with long-range dispersion correction. J. Comput. Chem., 2006. 27: p. 1787.4. Becke, A.D., Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals. J. Chem. Phys., 1997. 107: p. 8554.5. J. VandeVondele, et al., QUICKSTEP: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach. J. Comput. Phys. Commun., 2005. 167: p. 103.6. Klimes, J., D.R. Bowler, and A. Michaelides, Van der Waals density functionals applied to solids. Phys. Rev. B, 2011. 83: p. 195131.7. Brandon G. Cook, William R. French, and a.K. Varga, Electron Transport properties of carbon nanotube-graphene contacts. Appl. Phys. Lett., 2012. 101: p. 153501.

A Remodeled Protein Arginine Methyltransferase 1 (PRMT1) Generates Symmetric Dimethylarginine

Protein arginine methylation is emerging as a significant post-translational modification involved in various cell processes and human diseases. As the major arginine methylation enzyme, protein arginine methyltransferase 1 (PRMT1) strictly generates monomethylarginine and asymmetric dimethylarginine (ADMA), but not symmetric dimethylarginine (SDMA). The two types of dimethylarginines can lead to distinct biological outputs, as highlighted in the PRMT-dependent epigenetic control of transcription. However, it remains unclear how PRMT1 product specificity is regulated. We discovered that a single amino acid mutation (Met-48 to Phe) in the PRMT1 active site enables PRMT1 to generate both ADMA and SDMA. Due to the limited amount of SDMA formed, we carried out quantum mechanical calculations to determine the free energies of activation of ADMA and SDMA synthesis. Our results indicate that the higher energy barrier of SDMA formation (ΔΔG(‡) = 3.2 kcal/mol as compared with ADMA) may explain the small amount of SDMA generated by M48F-PRMT1. Our study reveals unique energetic challenges for SDMA-forming methyltransferases and highlights the exquisite control of product formation by active site residues in the PRMTs.

Parametrization of Atomic Energies to Improve Small Basis Set Density Functional Thermochemistry.

Enthalpies of formation predicted with density functional theory and small basis sets can be greatly improved by treating the atomic energies as empirical parameters. When a variety of functionals and small basis sets are used, the root-mean-square error in enthalpies of formation is reduced by a factor of approximately two for the least improved functional/basis set pair, with significantly larger reductions for other functionals, especially LSDA. When the 3-21G* and 3-21+G* basis sets are used with nonempirical functionals, it is possible to achieve accuracy greater than that of PM3, which was primarily designed to reproduce enthalpies of formation. In addition to decreasing statistical errors, our procedure can also remove qualitative errors in density functional/basis set pairs that fail for the prediction of enthalpies of formation.

Perspective on "Density functional thermochemistry. III. The role of exact exchange"

Perspective on "Density functional thermochemistry. III. The role of exact exchange"

Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals

A systematic procedure for refining gradient corrections in Kohn–Sham exchange-correlation functionals is presented. The procedure is based on least-squares fitting to accurate thermochemical data. In this first application of the method, we use the G2 test set of Pople and co-workers to generate what we believe to be an optimum GGA/exact-exchange density-functional theory (i.e., generalized gradient approximation with mixing of exactly computed exchange).

Accurate density functional thermochemistry for larger molecules

Density functional methods are combined with isodesmic bond separation reaction energies to yield accurate thermochemistry for larger molecules. Seven different density functionals are assessed for the evaluation of heats of formation, Delta H 0 (298 K), for a test set of 40 molecules composed of H, C, O and N. The use of bond separation energies results in a dramatic improvement in the accuracy of all the density functionals. The B3-LYP functional has the smallest mean absolute deviation from experiment (1.5 kcal mol/f).

Accurate density functional thermochemistry for larger molecules

Density functional methods are combined with isodesmic bond separation reaction energies to yield accurate thermochemistry for larger molecules. Seven different density functionals are assessed for the evaluation of heats of formation, Δ H f 0 (298 K), for a test set of 40 molecules composed of H, C, O and N. The use of bond separation energies results in a dramatic improvement in the accuracy of all the density functionals. The B3-LYP functional has the smallest mean absolute deviation from experiment (1·5 kcal mol f -1).

Density-functional thermochemistry. IV. A new dynamical correlation functional and implications for exact-exchange mixing

A new dynamical correlation functional is constructed subject to a small number of simple, yet key, requirements not all satisfied by existing functionals in the literature. The new functional gives good atomic correlation energies, and, in conjunction with previous gradient-corrected exchange functionals and exact-exchange mixing, excellent thermochemistry in the G2 benchmarks of Pople and co-workers.

Density-functional thermochemistry. III. The role of exact exchange

Despite the remarkable thermochemical accuracy of Kohn–Sham density-functional theories with gradient corrections for exchange-correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact-exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange-correlation functional containing local-spin-density, gradient, and exact-exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first- and second-row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.

Density-functional thermochemistry. II. The effect of the Perdew–Wang generalized-gradient correlation correction

In an earlier paper [A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], Kohn–Sham density-functional calculations of the total atomization energies of the 55 molecules of the Gaussian-1 database of Pople and co-workers [J. Chem. Phys. 90, 5622 (1989); 93, 2537 (1990)] were reported. We found that the local-spin-density exchange-correlation approximation with a ‘‘gradient correction’’ for exchange gave an average deviation from experiment of only 3.7 kcal/mol. In the present work we assess the role of gradient corrections for dynamical correlation, and we enlarge our earlier survey to include 42 atomic and molecular ionization potentials and 8 proton affinities as well. We conclude that gradient corrections for correlation do not improve atomization energies, but are vitally important in electron nonconserving processes such as ionization.

Density-functional thermochemistry. I. The effect of the exchange-only gradient correction

Previous work by the author on diatomic molecules and by others on polyatomic systems has revealed that Kohn–Sham density-functional theory with ‘‘gradient corrected’’ exchange-correlation approximations gives remarkably good molecular bond and atomization energies. In the present communication, we report the results of an extensive survey of density-functional atomization energies on the 55 molecules of the Gaussian-1 thermochemical data base of Pople and co-workers [J. Chem. Phys. 90, 5622 (1989); 93, 2537 (1990)]. These calculations have been performed by the fully numerical molecules (NUMOL) program of Becke and Dickson [J. Chem. Phys. 92, 3610 (1990)] and are therefore free of basis-set uncertainties. We find an average absolute error in the total atomization energies of our 55 test molecules of 3.7 kcal/mol, compared to 1.6 kcal/mol for the Gaussian-1 procedure and 1.2 kcal/mol for Gaussian-2.