{ "comment": "A synthetic chemistry paper, as first read, with the reading errors its corrections fix. Text written for this fixture; CC0-1.0.", "document": { "key": "hale2026harmonic", "store": "smithlab", "kind": "article", "work": {"key": "hale2026harmonic", "same_as": ["doi:10.5555/example.hale.2026"]}, "version": {"type": "version-of-record", "date": "2026-03-02"}, "relations": [], "meta": {"type": "article-journal", "title": "Harmonic bond parameters for small organic molecules from a two-step fit", "author": [{"family": "Hale", "given": "R."}, {"family": "Osei", "given": "M."}], "container-title": "Journal of Example Chemistry", "volume": "14", "page": "101-109", "issued": {"date-parts": [[2026, 3, 2]]}, "DOI": "10.5555/example.hale.2026"}, "language": "en", "license": {"text": "All rights reserved by the publisher (fictional)."}, "policy": "full" }, "legacy_aliases": {"b-p01-text-003": "@s3", "b-p02-table-001": "@tab1"}, "tree": {"kind": "document", "children": [ {"kind": "front", "page": 1, "children": [ {"kind": "title", "children": [{"s": ["Harmonic bond parameters for small organic molecules from a two-step fit"], "fidelity": "F2"}]}, {"kind": "authors", "runs": ["R. Hale and M. Osei"], "fidelity": "F2"}, {"kind": "abstract", "children": [{"p": [ {"s": ["We fit harmonic bond constants for twelve bonds in two steps, first to a scan and then to vibrational frequencies."], "fidelity": "F2"}, {"s": ["The two parameter sets agree to within 2% for every bond."], "fidelity": "F2"} ]}]} ]}, {"kind": "section", "name": "@sec1", "label": "1", "level": 1, "page": 1, "title": "Introduction", "children": [ {"p": [ {"name": "@s1", "s": ["Harmonic bond terms remain the most common description of covalent stretching in classical force fields.", {"cite": ["@r1"], "text": "1"}], "fidelity": "F2"}, {"name": "@s2", "s": ["The bond energy is given by ", {"eq": {"name": "@eq1", "label": "(l)", "tex": "E_{\\mathrm{bond}} = \\frac{1}{2} K_r (r - r_{\\mathrm{eq}})^2", "fidelity": "F1"}}, " where ", {"m": "K_r"}, " is the bond force constant and ", {"m": "r_\\mathrm{eq}"}, " the equilibrium bond length."], "fidelity": "F2"}, {"name": "@s3", "s": ["Water, H", {"m": "_2"}, "O, served as the first test case, with a bending band near 1595 cm⁻¹.", {"cite": ["@r2"], "text": "2"}], "fidelity": "F2"} ]}, {"p": [ {"name": "@s4", "s": ["Values below 10-3 kcal mol⁻¹ were treated as zero. ", {"xref": "@tab1", "text": "Table 1"}, " lists the fitted constants for both parameter sets."], "fidelity": "F0"} ]} ]}, {"kind": "section", "name": "@sec2", "label": "2", "level": 1, "page": 2, "title": "Methods", "children": [ {"name": "@para6", "p": [ {"name": "@s6a", "s": ["Each bond was scanned in steps of 0.01 Å around its minimum, and the energies were"], "fidelity": "F0"}, {"name": "@s6b", "s": ["fitted by least squares."], "fidelity": "F0"} ]}, {"name": "@para7", "p": [ {"name": "@s7", "s": [{"xref": "@fig1", "text": "Figure 1"}, " shows the scan for the C–C bond of ethane.", {"fn": "@fn1", "text": "a"}], "fidelity": "F2"} ]}, {"name": "@head2", "p": [{"name": "@rh", "s": ["J. Example Chem. 2026, 14, 101–109"], "fidelity": "F0"}]}, {"kind": "footnote", "name": "@fn1", "label": "a", "children": [{"name": "@fns", "s": ["Scans held every other coordinate fixed."], "fidelity": "F2"}]}, {"kind": "figure", "name": "@fig1", "label": "Figure l", "children": [ {"kind": "panel", "name": "@pa", "label": "a", "figure_text": [ {"text": "r (Å)", "role": "axis-label", "name": "@ft_x"}, {"text": "E (kcal mol⁻¹)", "role": "axis-label", "name": "@ft_y"}, {"text": "1.4", "role": "tick-label"}, {"text": "1.5", "role": "tick-label"}, {"text": "1.6", "role": "tick-label"} ]}, {"kind": "panel", "name": "@pb", "label": "b"}, {"kind": "caption", "children": [ {"name": "@cap1", "s": ["Bond energy along the C–C stretch of ethane."], "fidelity": "F2"}, {"name": "@cap2", "s": ["(a) The scan."], "fidelity": "F2"}, {"name": "@cap3", "s": ["(b) The residual of the fit."], "fidelity": "F2"} ]} ]}, {"kind": "table", "name": "@tab1", "label": "Table 1", "columns": [ {"name": "@col_bond", "header_path": ["@h_bond"]}, {"name": "@col_ak", "header_path": ["@h_a", "@h_ak"]}, {"name": "@col_ar", "header_path": ["@h_a", "@h_ar"]}, {"name": "@col_bk", "header_path": ["@h_b", "@h_bk"]}, {"name": "@col_br", "header_path": ["@h_b", "@h_br"]} ], "children": [ {"kind": "caption", "children": [{"s": ["Fitted harmonic bond parameters."], "fidelity": "F2"}]}, {"kind": "table-head", "children": [ {"row": [ {"name": "@h_bond", "c": ["Bond"], "role": "column-header", "rowspan": 2, "col": "@col_bond"}, {"name": "@h_a", "c": ["Set A"], "role": "column-header", "colspan": 2, "col": "@col_ak"}, {"name": "@h_b", "c": ["Set B"], "role": "column-header", "colspan": 1, "col": "@col_bk"} ]}, {"row": [ {"name": "@h_ak", "c": [{"m": "K_r"}, " (kcal mol⁻¹ Å⁻²)"], "role": "column-header", "col": "@col_ak"}, {"name": "@h_ar", "c": [{"m": "r_\\mathrm{eq}"}, " (Å)"], "role": "column-header", "col": "@col_ar"}, {"name": "@h_bk", "c": [{"m": "K_r"}, " (kcal mol⁻¹ Å⁻²)"], "role": "column-header", "col": "@col_bk"}, {"name": "@h_br", "c": [{"m": "r_\\mathrm{eq}"}, " (Å)"], "role": "column-header", "col": "@col_br"} ]} ]}, {"kind": "table-body", "name": "@body", "children": [ {"row": [{"name": "@grp", "c": ["Bond parameters"], "role": "row-group-header", "colspan": 5, "col": "@col_bond"}]}, {"name": "@row_cc", "header_path": ["@grp", "@cc"], "row": [ {"name": "@cc", "c": ["CT–CT"], "role": "row-header", "col": "@col_bond"}, {"name": "@cc_ak", "c": ["3l0.0"], "col": "@col_ak", "fidelity": "F0"}, {"name": "@cc_ar", "c": ["1.526"], "col": "@col_ar"}, {"name": "@cc_bk", "c": ["305.2"], "col": "@col_bk"}, {"name": "@cc_br", "c": ["1.5260"], "col": "@col_br"} ]}, {"name": "@row_ch", "header_path": ["@grp", "@ch"], "row": [ {"name": "@ch", "c": ["CT–HC"], "role": "row-header", "col": "@col_bond"}, {"name": "@ch_ak", "c": ["340.0"], "col": "@col_ak"}, {"name": "@ch_ar", "c": ["1.090"], "col": "@col_ar"}, {"name": "@ch_bk", "c": ["338.7 1.0900"], "col": "@col_bk", "fidelity": "F0"} ]} ]}, {"kind": "table-note", "children": [{"s": ["Set B was refitted with half the step size."], "fidelity": "F2"}]} ]} ]}, {"kind": "back", "page": 2, "children": [ {"kind": "references", "children": [ {"kind": "reference", "name": "@r1", "label": "1", "runs": ["(1) A. 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