used Open Babel 56 to perceive connectivity and generate a SMILES for the reactant and product from each set of three-dimensional coordinates. The input and output for the growing string method are a set of three-dimensional coordinates to describe the molecule or multi-molecule complex. 42 used the single-ended growing string method 44 to generate a list of possible products from a given reactant. Finally, we identify a subset of reactions that contain rigid species, calculate high-pressure limit TST rate coefficients, and report the fitted Arrhenius parameters. Similarly, enthalpies of reaction are calculated based on the difference of the ZPE-corrected product and reactant energies bond additivity corrections (BACs) are added to each species. These energies are used to calculate updated barrier heights by adding the zero-point energies (ZPEs) from the harmonic vibrational analysis to the reactant, product, and TS energies and then computing the difference between the resulting TS and reactant energies. The single point energy of all species optimized at ωB97X-D3/def2-TZVP is computed at CCSD(T)-F12a/cc-pVDZ-F12. Next, product complexes are separated into individual species, each of which is reoptimized at the respective level of theory i.e. We also report accurate transition state theory rate coefficients \((T)\) or Arrhenius parameters for reactions involving flexible reactants or transition states since RRHO TST is not accurate for these reactions.ĭataset refinement started by cleaning the SMILES from the original dataset 43 and filtering reactions to those containing one reactant and at most three products. Our higher-accuracy coupled-cluster barrier heights differ significantly (RMSE of ∼5 kcal mol −1) relative to those calculated at ωB97X-D3/def2-TZVP. These reactions involve H, C, N, and O, contain up to seven heavy atoms, and have cleaned atom-mapped SMILES. We report the results from these quantum chemistry calculations and extract the barrier heights and reaction enthalpies to create a kinetics dataset of nearly 12,000 gas-phase reactions. Here, we use CCSD(T)-F12a/cc-pVDZ-F12// ωB97X-D3/def2-TZVP to obtain high-quality single point calculations for nearly 22,000 unique stable species and transition states. However, such data are often difficult to find, and high-quality datasets are especially rare. This is the molecular weight that is typically observed by electrospray mass spectrometry run in negative ion mode.Quantitative chemical reaction data, including activation energies and reaction rates, are crucial for developing detailed kinetic mechanisms and accurately predicting reaction outcomes.
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The protonated molecular weight is also typically equal to the backbone weight plus the total number of phosphates multiplied by 1.01 for each proton (H+). Note that some modifications add additional phosphate groups to the molecular weight calculation, such as a 3’ phosphate modification or 3’ thymidine linked modifications. The weight of each counter ion is generally assumed to 102.2 for Triethylammonium (TEA). This added weight is typically equal to the number of phosphates in the oligo multiplied by the weight of the counter ion. The addition of counter ions is simply the molecular weight backbone plus the total weight of counter ions. MWHAdj = 0, 1, or 2 protons (i.e., 0, 1.01, or 2.02), depending on the presence and structure of 3' and 5' modifications.
This is the MW for that portion of a phosphate linkage not already included in MWbase or MWmod. MWPO2 = molecular weight of PO2, i.e., 62.97.nPO2 = total count of internal phosphates, i.e., nbases + nmods - 1.MWMod = molecular weight of the deprotonated form of each individual modification.MWbase = molecular weight of the deprotonated nucleoside.Molecular weight backbone (g/mol) is calculated using the following formula: MW(backbone) = Σ(nbase * MWbase) + MW Modifications + (nPO2 * MWPO2) + MWHAdj *The extinction coefficient values for all other bases and modifications can be found on under the "Technical Specs" tab available for each oligo modification, or by downloading this PDF. All ε260 values are reported in units of M -1.Extinction Coefficient Calculation - The extinction coefficient is calculated with the following method: ε260 = x 0.9, to adjust for hyperchromicity. The OligoSpec calculator outputs the physical properties for a particular oligo design.
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