- KenX2025
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KenX2025d.exe, Updated May 22, 2025
KenX2025d is supplied here free of charge to academics (including students), provided it is acknowledged. Commercial users require a special permission of the author. The users should quote the following reference:
Sakai, K. (2025). Kyushu University, Japan. KenX.
Crystallography
TThis software package has undergone continuous improvement through repeated revisions over the past two decades. A diverse range of practical routines has been implemented to enhance its functionality. Within this crystallographic interface, users can generate all necessary publication materials by integrating with the Shelxt and Shelxl programs for structure solution and refinement. Final publication-ready CIF files are generated almost automatically. Currently, the package is optimized for Rigaku output files; however, support for other instruments can be integrated upon request.
Handling Orthogonal Coordinates
1. Support for reading CIF files.
2.Capability to import and extensively modify orthogonal coordinates of molecules (e.g., from DFT calculations).
3. Tools for adding substituents and performing conformational adjustments, such as bond stretching and angle twisting.
4. Support for reading additional fragments randomly added to coordinate files; these fragments can be positioned relative to the main structure to generate initial configurations for DFT optimization.
Multi-columned Table for Crystallographic Data
Program called CrysTab.exe can be utilized for this purpose.
Multi-columned Table for Crystallographic Data
Program called HKLConv.exe can be used to relocate the columnar order of the h k l for reflection data. For orthrombic crystal systems, miselection of the h k l often cause difficulty in solving the structure. After passing your data for checking in Platon, you maight be requested to changes the arrangement of your abc vectors. In such a case this program can be used to rearrange the order of h k l in your reflection data.
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- GaussianConv2025
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GaussianConv2025.exe, Update on February 9, 2025
Gloabl Tool for Gaussian 03/09/16
1. Log File Support: Reads output files (*.log or *.out) generated by Gaussian 03, 09, and 16.
2. Optimization Monitoring: Automatically extracts SCF energies during or after an optimization (Opt) run to plot the energy minimization profile.
a. Access: Navigate to "View Results" and select "SCF Energy Change Profile (Opt)".
b. Structure Export: Upon "Normal Termination", the final optimized geometry can be saved in Cartesian format by selecting the final frame and clicking the save button.
v. Convergence Metrics: Graphically plots Maximum/RMS Force and Maximum/RMS Displacement.
d. Troubleshooting: If the energy profile fluctuates (up-and-down behavior) without reaching convergence, the user should abort the calculation and revise the input parameters for a re-run. The strategy in 3c below may help resolve these issues.
3. Transition State (TS) Verification: Even with a normal termination, the structure may settle into a TS rather than a local minimum.
a. Frequency Analysis: Verify the absence of imaginary (negative) frequencies. Navigate to "View Results" and select "Frequencies, Energies, etc. (Opt)". The data in this window can be saved as a report for your publication's ESI (Electronic Supplementary Information).
b. Handling Negative Frequencies: If negative frequencies are present, users should first examine the vibrational modes using GaussView or an equivalent platform to determine the proper direction for structure refinement.
c. Advanced Refinement: Alternatively, users can re-run the optimization by adding the CalcFC or CalcAll keywords to the Opt command, employing a more rigorous algorithm to bypass the TS domain and find the true minimum.
4. Simulating TD-DFT Spectra:Reading a log file from a completed TD-DFT calculation enables the "Spectra (TD-DFT Results)" option under the "View Results" menu. This feature produces simulated spectra across various absorbance vs. energy scales.
a. Figure Preparation for Publication: Users can adjust plotting modes, font styles, and label sizes to generate optimized figures. These can be screen-captured for direct use in publication materials.
b. Transition Analysis: Within the spectral window, [Ctrl + Mouse-Click] (left button) on an oscillator strength bar to display the major configurations (CI coefficients) involved in that transition. This is a powerful tool for identifying the character of each electronic transition.
5. Viewing Multiple MO Diagrams: Navigate to "View Results" and select "MO Energy Table/Diagram". This feature allows users to compare the molecular orbital (MO) energy levels of multiple analogous compounds side-by-side.
6. Ploting Projected Density of States (PDOS): To utilize this routine effectively, molecular orbital (MO) calculations must be performed using the keywords "GFPRINT" and "Pop=Full".
a. GFPRINT allows the program to extract the names of all Atomic Orbitals (AOs) used in the basis set.
b. Pop=Full generates the complete 2D MO coefficient table.
c. Note on Precision: Since the coefficients extracted from the log file have limited numerical precision (fewer digits), it is highly recommended to import the more precise coefficients from the corresponding FCH file generated at the final stage of the calculation.
c. Saving MO Coefficient Table for Excel: The table can be saved as a text file (*.txt) with numerical values separated by TAB delimiters for easy importation into spreadsheet software.