NCI-Lens 🔬

3D Viewer and Analyzer of Noncovalent Interactions

📦 DOI: 10.5281/zenodo.22017076 | Version: 5.1

NCI-Lens is a fast, browser-based 3D molecular viewer designed for crystallographers, computational chemists, and students. It automatically detects, visualizes, and estimates the energy of a wide spectrum of noncovalent interactions (NCIs) directly from structural files.

With the v5.1 update, NCI-Lens introduces unprecedented accuracy in $\pi$-hole and $\sigma$-hole detection, featuring advanced geometric shadow guards, SAPT-like energy decomposition, and specialized calibrations for anion-$\pi$ complexes and metallylenes.

🌐 Launch Web App (No installation required, runs entirely in your browser)

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🚀 What's New in v5.1 (Advanced $\pi$-hole & Shadow Guards)

• Advanced $\pi$-hole Hygiene & Shadow Guards: Implemented strict geometric guards to eliminate false positives and double-counting:
  • Reverse $n \to \pi^*$ guard: Prevents carboxyl/ester oxygens from falsely acting as carbonyl $\pi$-acceptors.
  • 1,2-shadow & $\sigma$-donor shadow guards: Distinguishes genuine lone-pair attacks from the geometric shadows of adjacent $\sigma$-hole bonds.
• Angular Anomaly Calibration: Precise tilt-axis calibrations for non-standard $\pi$-hole donors, including square-planar XeF₄ (25° tilt) and bent SeO₂ (4° tilt).
• Lone-Pair Penalties & Metallylenes: Energy scaling dynamically adjusts based on the donor's lone-pair count. Added massive binding energy boosts for metallylenes (SiH₂, GeH₂) acting as $\pi$-hole donors.
• Anion-$\pi$ & Charge-Assisted Complexes: Dedicated SAPT regime switching and energy multipliers for anionic nucleophiles binding to $\pi$-holes.
• Hydridic $\to$ $\pi$ Interactions: Full support for nucleophilic hydridic hydrogens (bonded to B, Al, Si, metals) interacting with aromatic rings and other $\pi$-systems.
• Pentacoordinate Tetrel Bonds: Broadened angular wells (~90–110°) to accurately model charge-assisted tetrel attacks.
• Onium & Planar Nitrogen Exclusion: Quaternary/planar nitrogens and covalently bound halogens are now correctly excluded from acting as $\pi$-acceptors.
• Refined Coulomb Screening: Optimized $\pi$-path Coulomb screening to prevent overestimation of oxoanion and nitrate contacts.

✨ Key Features

• Comprehensive NCI Detection: Automatically finds Hydrogen bonds, Halogen, Chalcogen, Pnictogen, Tetrel, Triel, Aerogen, and $\pi$-hole bonds, as well as $\pi$-stacking.
• SAPT-like Energy Decomposition: Energies are split into Electrostatics (ES), Induction (IND), and Dispersion (DISP) components, exportable via IUCr CSV.
• Crystal Walking: Clicking a "ghost sphere" of a hidden partner atom clones the fragment at the contact site, allowing you to visually "walk" through infinite crystal lattices.
• Smart UI: 9 individual toggle buttons for each NCI type. Dragged labels remember their positions. Pointer lines intelligently stop at the text boundary to avoid overlapping.
• Multi-language: Full localization support for English, Russian, and Portuguese (Brasil).

🔗 Supported Interactions

Type	Description	Visual
H-bond	Classic D–H···A electrostatic + dispersion	Blue dashed
Aerogen	$\sigma$-hole on Kr, Xe, Rn	Teal dashed
Halogen	$\sigma$-hole on Cl, Br, I, At (incl. hypervalent)	Violet dashed
Chalcogen	$\sigma$-hole on S, Se, Te, Po (incl. hypervalent)	Yellow dashed
Pnictogen	$\sigma$-hole on P, As, Sb, Bi (incl. hypervalent)	Orange dashed
Tetrel	$\sigma$-hole on C (activated), Si, Ge, Sn, Pb	Green dashed
Triel	$\sigma$-hole / $\pi$-hole on B, Al, Ga, In, Tl	Pink dashed
$\pi$-hole	Carbonyls, CO₂, NO₂, perfluorinated rings, metallylenes	Magenta dashed
$\pi$-stack	Aromatic ring stacking (excluding sp³)	Green centroid lines

📂 Supported File Formats

• .cif (Full crystallographic support: unit cells, symmetry operations, anisotropic thermal ellipsoids. Intermolecular contacts across symmetry boundaries are automatically detected and glued via BFS).
• .xyz (Standard and Chem3D, supports trajectories)
• .pdb, .mol, .sdf

🖱️ Controls

• Rotate: Left Mouse Button / 1-finger touch
• Zoom: Scroll Wheel / Pinch
• Pan: Right Mouse Button / 3-finger touch / On-screen Joystick
• Measure: Click atoms sequentially (2 for distance, 3 for angle, 4 for torsion).
• Isolate Fragment: Click an atom ➔ press ⛶ Fragment.
• Multi-select: Shift + Click atoms across different molecules, then isolate.

⚛️ Scientific Background & Calibration

The energy estimation model (accessible via the PRO button in the app) relies on empirical geometric parameters, EQeq charges, and explicit polarization/charge-transfer terms.

• Calibration: The model was calibrated against 113 literature associates (spanning $\sigma$-hole, $\pi$-hole, and $\pi$-stacking interactions) using high-level quantum chemistry benchmarks (SAPT, DLPNO-CCSD(T), QTAIM).
• Accuracy: Median absolute error is ~3 kJ/mol for weak contacts. For stronger contacts, 60% of the dataset shows an error of <10%.
• Thresholds: Interactions below the user-defined threshold (default 2 kJ/mol / 0.5 kcal/mol) are hidden to reduce visual clutter but are accounted for in the total energy sum. Contacts exceeding 150 kJ/mol are flagged as having significant covalent character.

👨‍🔬 Credits & Citation

Developed by BOLLAB (Dmitrii S. Bolotin). If you use NCI-Lens in your research, please cite the repository and the underlying geometric models for $\sigma$/$\pi$-hole interactions. A comprehensive list of the 37 foundational papers used for calibration is available in the in-app PRO documentation window.

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© 2021-2026 BOLLAB. Released under MIT License.