A theoretical study of C4H5N isomers: Comparison of cyano and isocyano as substituents

Ab initio molecular orbital calculations using a 3-21G basis set have been used to optimize geometries for pyrrole, CH₃(X)CCH₂, CH₃(H)CCHX (both cis and trans), c-C₃H₅X, and CH₂CHCH₂X, where X is CN and NC. In all the alkenyl derivatives methyl groups are found to adopt the conformation in which the methyl hydrogen eclipses the double bond. 6-31G*∥3-21G level calculations show the alkenyl cyanides to be of similar energy to pyrrole, but the isocyanides are ～20 kcal mol^?1 higher in energy. For both substituents the cyclopropyl derivatives are higher in energy by ～10 kcal mol^?1. At the 6-31G* level ring strain is 27.7 kcal mol^?1 for the cyanide and 30.6 kcal mol^?1 for the isocyanide. Data on the relative energies of RCN and RNC are compared when R is (i) a saturated hydrocarbon, (ii) an unsaturated hydrocarbon, (iii) an α-carbenium ion, (iv) an allyl cation, and (v) an α-carbanion.     

Ab initio molecular orbital calculations for 3,6-dihydro-1,2-dithiin and 3,6-dihydro-1,2-dioxin

Optimized geometries and total energies for the conformers of 3,6-dihydro-1,2-dithiin ( 2 ) and 3,6-dihydro-1,2-dioxin ( 3 ) were calculated at several ab initio MO levels: RHF/3-21G(*), RHF/6-31G*, MP2/6-31G*, and MP2/6-31G*/ /RHF/3-21G(*). For the dioxin, in addition to the above levels the corresponding nonextended basis sets ab initio methods were also carried out. The dithiin results are compared with those of simple disulfanes, HSSH and (CH₃)₂S₂, whose optimized geometries agree closely with the observed structures, which is the gauche (C₂ symmetry). For the disulfanes, the gauche geometries from RHF/3-21G(*) are in good agreement with the observed structure while the RHF/3-21G results best fit the dioxin. Pertinent structural data at the RHF/3-21G(*) for the half-chair (C₂) dithiin are: bond lengths, ? SS? , ? CS? , ? CC?, and ? C?C? , 2.050, 1.817, 1.515, and 1.317 Å, respectively; bond angles, CSS, ?CCS, and C?CS, 98.0, 114.2, and 127.8°, respectively; CSSC dihedral angle of 63.2°; and twist angle of 36.5°. The total energy for half-chair dithiin at MP2/6-31G*//RHF/3-21G(*) is less than the planar (C_2v) and the half-boat (C_s) structures by 69.67 and 29.05 kJ/mol, respectively. The calculated structural data (vs. observed) at RHF/3-21G for the half-chair dioxin are: bond lengths, ? OO? , ? CO? , ? CC?, and C?C, 1.464 (1.463), 1.454, 1.509, and 1.313 Å (1.338 Å), respectively; bond angles, COO, ?CCO, and C?CO, 105.0, 109.8 (110.3), and 120.7° (119.9°), respectively; COOC dihedral angle of 79.7° (80 ± 2°); and twist angle of 39.0 (38.3°). The total energy for half-chair dioxin at MP2/6-31G//RHF/3-21G is less than the planar and the half-boat structures by 70.35 and 42.85 kJ/mol, respectively. The total energies calculated at the extended basis sets (*) ab initio levels for the C₂ symmetry dioxin are much lower than those of the nonextended basis sets. © John Wiley & Sons, Inc.     

Theoretical studies of organometallic compounds. II. All electron and pseudopotential calculations of M(CH3)nCl4 − n (M = C,Si, Ge,Sn, Pb; n = 0–4)

The performance of effective core potentials (ECP) for the main group elements of group IV has been studied by calculating the geometries and reaction energies of isodesmic reactions for the molecules M(CH₃)_nCl_{4 ? n} (M = C, Si, Ge, Sn, Pb; n = 0–4) at the Hartree–Fock level of theory. The results are compared with data from all electron calculations and experimental results as far as available. The all electron calculations were performed with a 3-21G(d) and a 6-31G(d) basis set for Si, a (43321/4321/41) basis set for Ge, and a (433321/43321/431) basis set for Sn. For the ECP calculations the potentials developed by Hay and Wadt with a configuration (n)s^a(n)p^b and the valence basis set (21/21), extended by a set of d functions, are employed. © 1992 by John Wiley & Sons, Inc.     

Molecular structures and intramolecular interactions in dimethyl cyclohexane isomers

The geometries of ten isomers of dimethyl cyclohexane were determined by ab initio gradient geometry refinement with the 4-21G basis set. It is found that many intramolecular interactions are clearly manifested by correlated structural trends, and that they are consistent with strain energies calculated by employing previously defined ab initio group equivalents. Specifically, non-bonded interactions are found between two adjacent methyl groups in some of the forms, and between axial methyl groups and adjacent axial C? H bonds in others. Unperturbed axial C? H and C? C bonds are consistently longer than equatorial bonds. In general, C? H bonds which are involved in non-bonded repulsive interactions are shortened, i.e., strengthened, and the corresponding H? C? C angles are large, compared to non-interacting parameters.     

A theoretical study of α-substituted isopropyl and cyclopropyl anions

Ab initio molecular orbital theory has been used to probe the effect of the substituent X on the structures, strain energies, stabilization energies, inversion barriers, and proton affinities of carbanions CH₃CX CH and cis-C₃H₄X^?, where X = H, F, CN, and NC. All geometries have been optimized with a 3-21G basis set, and the parent anions (X = H) were also optimized with the same basis set with a diffuse function added (i.e. the 3-21 + G basis set). The anions, with the exception of the α-cyanoisopropyl anion, are pyramidal. The out-of-plane angle, α, for the pyramidal anions decreases in the order F > H ≈ NC > CN, and the barriers to inversion follow the same order with the cyclopropyl anions consistently having higher barriers than the isopropyl anions. The substituents strongly stabilize the anions with the stabilization energy following the order CN > NC > F. The cyano group slightly reduces the strain energy of cyclopropane, but the isocyano and fluoro substituents are weakly and strongly destabilizing, respectively. The pyramidal cyclopropyl anions are less strained than the cyclopropanes except when the substituent is a cyano group where the strain energies are reversed but are very similar. The planar anions all have higher strain energies than the cyclopropanes.     

Theoretical Investigations on Fluorine-Substituted Ethylene Dications C2HnF4-n 2+(n = 0–4)

The optimized geometries and energies of fluorine-substituted ethylene dications C₂H_nF_4-n ²⁺ (n = 0–4) have been investigated by means of ab initio methods. At the MP3/6-31G**//6-31G* + zero-point energy level of theory, the results predict that C₂F₄²⁺ and C₂HF₃²⁺ are planar, while C₂H₄²⁺, C₂H₃F²⁺ and 1,1—C₂H₂F₂²⁺ prefer a perpendicular geometry. For 1,2—C₂H₂F₂²⁺ an energy difference of only 0.3 kcal/mol is found between the (trans) planar and perpendicular structure. The stabilizations attributed to hyperconjugation, fluorine lone-pair donation, and (C? F) double-bond conjugation are discussed. A comparison is made for the C? C and C? F stretching frequencies determined at 6-31G*//6-31G* between the neutral and dicationic species. The theoretically determined ionization energies for the vertical process N⁺ → N²⁺ at the MP3/6-31G*//3-21G level are compared with experimental Q_min values.     

Ab initio studies of structural features not easily amenable to experiment. 25. Conformational analysis of methyl propanoate and comparison with the methyl ester of glycine

The molecular geometries of three conformations of methyl propanoate (MEP) (C? C? C?O torsions of 0°, 120°, and 180°) and the potential-energy surfaces of MEP (C? C? C?O torsions) and of the methyl ester of glycine (MEG) (N? C? C?O torsions) have been determined by ab initio gradient calculations at the 4-21G level. MEP has conformational energy minima at 0° and 120° of the C? C? C?O torsion, while the 60–90° range and 180° are energy maxima. For MEG there are two minima (at 0° and 180°) and one barrier to N? C? C?O rotation in the 60–90° range. The N? C? C?O barrier height is about twice as high (4 kcal/mol) as the C? C? C?O barrier. The 180° N? C? C?O minimum is characteristically wide and flat allowing for considerable flexibility of the N? C? C?O torsion in the 150–210° range. This flexibility could be of potential importance for polypeptide systems, since the N? C? C?O angles of helical forms are usually found in this region. The molecular structures of the methyl ester group CH₃OC(?O)CHRR′ in several systems are compared and found to be rather constant when R ? H and R′ ? H, CH₃, CH₃CH₂; or when R ? NH₂ and R′ ? H, CH₃, or CH(CH₃)₂.     

The anomeric effect: Ab-initio studies on molecules of the type X?CH2?O?CH3

The anomeric effect of the functional groups X = C?N, C?CH, COOH, COO^?, O? CH₃, NH₂, and NH⁺₃ has been studied with ab initio techniques. Geometry effects upon rotation around the central C? O bond in X? CH₂? O? CH₃ have been compared in the various compounds. The energy differences between the conformers with a gauche and trans (X? C? O? C) arrangement were calculated at the 6-31G* level in the fully optimized 4-21G geometries. Energy differences calculated at the 4-21G level appeared not to be reliable, especially for the groups X that contain non-sp³ hybridized atoms. The 6-31G* energy differences indicate a normal anomeric effect for X = COO^?, O? CH₃, and NH₂(g⁺) (ca. 13 kJ/mol) and a small anomeric effect for X = COOH, C?N, and C?CH (ca. 6 kJ/mol). For X = NH₂(t) and NH⁺₃ a reverse anomeric effect occurs. These observations are in line with experimental results and evidence is given for a competition among various stereoelectronic interactions that occur at the same anomeric center. Geometry variations can be understood in terms of simple rules associated with anomeric orbital interactions. Trends followed when the group X is varied cannot be related in a straightforward way to the energy differences between the trans and the gauche forms in these compounds. Only the variation in the gauche torsion angle X? C? O? C follows roughly the same trend.     

A DFT study of hydride transfers to the carbonyl oxygen of DDQ

Hydride‐transfer reactions between benzylic substrates and 2,3‐dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ) were investigated by DFT (density functional theory) calculations. The lowest unoccupied molecular orbital of DDQ has the largest extension on two carbonyl oxygens, which comes from two‐step mixing of antisymmetric orbitals of fragment π MOs. Transition‐state (TS) geometries and activation energies of reactions of four benzylic substrates R²? CH₂‐para‐C₆H₄? R¹ (R¹, R² = H and/or OCH₃) with DDQ were calculated. M06‐2X/6‐311(+*)G* was found to be a practical computational method, giving energies and geometries similar to those of M06‐2X/6‐311++G(3df,2pd) and wB97xD/6‐311++G(3df,2pd). For toluene (R¹ = R² = H), an initiation‐propagation model was suggested, and the calculated kinetic isotope effect k(H)/k(D) = 5.0 with the tunnel correction at the propagating step is in good agreement with the experimental value 5.2. A reaction of para‐MeO? C₆H₄? CH₂(OMe) + DDQ + (H₂O)₁₄ → para‐MeO? C₆H₄? C(?O)H + HOMe + DDQH₂ + (H₂O)₁₃ was investigated by M06‐2X/6‐311(+*)G*. Four elementary processes were found and the hydride transfer (TS1) is the rate‐determining step. The hydride transfer was promoted by association with the water cluster. The size of the water cluster, (H₂O)_n, at TS1 was examined. Three models of n = 14, 20, and 26 were found to give similar activation energies. Metal‐free neutral hydride transfers from activated benzylic substrates to DDQ were proposed to be ready processes both kinetically and thermodynamically. © 2015 Wiley Periodicals, Inc.     

Critical comparison of the ab initio and spectroscopic methyl-C?H bond length difference in acetyl compounds,CH3C(O) X

In order to provide additional data for the relative lengths of methyl-C? H bond distances in acetyl derivatives, which are difficult to determine accurately by the conventional tools of structural chemistry, the geometries of CH₃COH, CH₃COF, CH₃COCH₃, CH₃COOH, and CH₃CONH₂ were determined by ab initio SCF gradient optimization at the 5-31G** level and compared with previous 4-21G results. For acetaldehyde 6-311G⁴* calculations were also performed and the correlated methyl-C? H stretching potential energy functions were determined. It is found that the calculated differences between the in-plane and out-of-plane methyl-C? H bonds are practically independent of the computational scheme. The calculated results are in contrast to relative bond lengths obtained by some vibrational overtone spectroscopic studies, but are in perfect agreement with C? H bond length differences determined from isolated C? H stretching frequencies of partially deuterated compounds. The reliability of the latter, and other spectroscopic data concerning the assignment of the methyl-C? H vibrations are critically analyzed. On the basis of the available evidence we conclude: (1) the methyl groups of the CH₃C(?O)X systems here discussed contain one strong (in-plane) and two weak (out-of-plane) C? H bonds; (2) intensities of C? H local mode spectra do not provide a reliable basis for assignment to individual bonds.     

1H and 13C NMR study of α-acetylenic PIII and PIV derivatives. Signs and magnitudes of J(P?C) and J(P?H)

All J(P? H) and J(P? C) values, including signs, have been obtained in acetylenic and propynylic phosphorus derivatives, R₂P(X)? C?C? H and R₂P(X)? C?C? CH₃ (X ? oxygen, lone pair and R ? C₆H₅, N(CH₃)₂, OC₂H₅, N(C₆H₅)₂, Cl) from ¹H and ¹³C NMR spectra. In P^IV derivatives the following signs are obtained: ¹J(P? C)+, ²J(P? C)+, ³J(P? C)+, ³J(P? H)+, ⁴J(P? H)? . Linear relations are observed between ¹J(P? C), ²J(P? C) and ³J(P? C) versus ³J(P? H), indicating that these coupling constants are mainly dependent on the Fermi contact term, though the other terms of the Ramsey theory do not seem to be negligible for ¹J(P? C) and ²J(P? C). In P^III derivatives these signs are: ¹J(P? C)- and +, ²J(P? C)+, ³J(P? C)-, ³J(P? H)-, ⁴J(P? H)+. Only ³J(P? C) and ³J(P? H) reflect a small contribution of the Fermi contact term while in ¹J(P? C) and ²J(P? C) this contribution seems to be negligible relative to the orbital and/or spin dipolar coupling mechanisms.     

Proton and sodium ion affinities of glycine and its sodium salt in the gas phase. Ab initio calculations

The energies of protonation and Na⁺ cationization of glycine (GLY) and its (GLY ? H + Na) salt in the gas phase were calculated using ab inltio calculations. The proton affinity of GLY, valued at the MP2/6–31G*//3-21G level, is 937 kJ mol^?1. The amino function is confirmed to be the most favourable site of protonation: ‘proton affinities’ of the carbonyl and hydroxyl functions are calculated to be 75 and 180 kJ mol^?1, respectively, lower than that of NH₂ at the MP2/6-31G*//3–21G level. Calculations performed up to the MP2/6–31G*//3–21G level give the Na⁺ affinity of GLY as 189 kJ mol^?1 and the H⁺ and Na⁺ affinities of (GLY – H + Na) as 1079 and 298 kJ mol^?1, respectively. The geometries of all neutral and protonated species optimized with the 3–21G basis set are described. Both H* and Na⁺ cations complex preferably between the nitrogen atom and the carbonyl oxygen atom, leading to pseudo-five-membered ring structures in which Na? O and Na? N bonds lengths are greater than 2 Å.     

Intrinsic Acid–Base Properties of a Hexa‐2′‐deoxynucleoside Pentaphosphate,d(ApGpGpCpCpT): Neighboring Effects and Isomeric Equilibria

The intrinsic acid‐base properties of the hexa‐2′‐deoxynucleoside pentaphosphate, d(ApGpGpCpCpT) [=(A1?G2?G3?C4?C5?T6)=(HNPP)^5?] have been determined by ¹H NMR shift experiments. The pK_a values of the individual sites of the adenosine (A), guanosine (G), cytidine (C), and thymidine (T) residues were measured in water under single‐strand conditions (i.e., 10 % D₂O, 47 °C, I=0.1 M , NaClO₄). These results quantify the release of H⁺ from the two (N7)H⁺ (G?G), the two (N3)H⁺ (C?C), and the (N1)H⁺ (A) units, as well as from the two (N1)H (G?G) and the (N3)H (T) sites. Based on measurements with 2′‐deoxynucleosides at 25 °C and 47 °C, they were transferred to pK_a values valid in water at 25 °C and I=0.1 M . Intramolecular stacks between the nucleobases A1 and G2 as well as most likely also between G2 and G3 are formed. For HNPP three pK_a clusters occur, that is those encompassing the pK_a values of 2.44, 2.97, and 3.71 of G2(N7)H⁺, G3(N7)H⁺, and A1(N1)H⁺, respectively, with overlapping buffer regions. The tautomer populations were estimated, giving for the release of a single proton from five‐fold protonated H₅(HNPP)^±, the tautomers (G2)N7, (G3)N7, and (A1)N1 with formation degrees of about 74, 22, and 4 %, respectively. Tautomer distributions reveal pathways for proton‐donating as well as for proton‐accepting reactions both being expected to be fast and to occur practically at no “cost”. The eight pK_a values for H₅(HNPP)^± are compared with data for nucleosides and nucleotides, revealing that the nucleoside residues are in part affected very differently by their neighbors. In addition, the intrinsic acidity constants for the RNA derivative r(A1?G2?G3? C4?C5?U6), where U=uridine, were calculated. Finally, the effect of metal ions on the pK_a values of nucleobase sites is briefly discussed because in this way deprotonation reactions can easily be shifted to the physiological pH range.     

Geometry optimization and electronic structures of molecules H_3AXAH_3

The geometries of molecules H_3AXAH_3(X=O,S,Se and A=C,Si)have been optimizedusing STO-3G ab initio calculations and gradient method and the results are in good agreement withreported experimental values.From the STO-3G optimized geometries,we have also calculated theelectronic structures of these molecules using 4-31G and 6-31G basis sets to obtain the MO energies.atomic net charges and dipole moments.The ionization potentials calculated by 6-31G basis set are ingood agreement with experimental values.     

Conformational study of phosphoserine in aqueous solutions. II—1H n.m.r. results

The 270 MHz n.m.r. spectra of phosphoserine (PSer) have been measured and completely analysed for seven pD values. The resulting vicinal coupling constants ³J(HαHβ) and ³J(PHβ) are used to discuss the conformations of PSer with respect to the (Hα)? Cα? Cβ? (O) and (Cα)? Cβ? O? (P) bond axes. The all-trans conformer predominates for all pD values, with its fractional population being minimal at pD values close to neutrality. The Cβ? O bond rotamer populations agree reasonably well with those obtained from ¹³C investigations.     

Theoretical studies of organometallic compounds. III. Structures and bond energies of FeCHn and FeCH (n = 1, 2, 3)

The geometries and dissociation energies for the Fe? C and C? H bonds of FeCH_n and FeCH (n = 1, 2, 3) have been calculated by ab initio quantum mechanical methods using different effective core potential models and Møller–Plesset perturbation theory. The HW3 ECP model, which has a configuration [core] (n?1)s², (n?1)p⁶, (n?1)d¹, (n)s^m for the transition metals, is clearly superior to the larger core LANL1DZ ECP model with the configuration [core] (n?1)d¹, (n)s^m. The Fe? C bond energies calculated at correlated levels using the HW3 ECP are in much better agreement with experiment than the LANL1DZ results. This effect is mainly due to the higher number of correlated electrons rather than the inclusion of the outermost core electrons in the Hartree–Fock calculation. At the PMP4/HW3TZ/6-31G(d)//MP2/HW3TZ/6-31G(d) level, the theoretically predicted Fe? C bond energies for FeCH are in the range of 80% of the experimental values and have nearly the same accuracy as all-electron calculations using large valence basis sets and the MCPF method for the correlation energy. © 1992 by John Wiley & Sons, Inc.     

Theoretical studies of organometallic compounds. I. All electron and pseudopotential calculations of Ti(CH3)nCl4 − n (n = 0–4)

The performance of effective core potentials (ECP) and model potentials (MP) has been studied by calculating the geometries and reaction energies of isodesmic reactions for the molecules Ti(CH₃)_nCl_{4 ? n} (n = 0–4) at the Hartree–Fock level of theory. The results are compared with data from all electron calculations and experimental results as far as available. The all electron calculations were performed with a 3-21G basis set from Hehre and a (53321/521/41) basis set from Huzinaga. For the ECP calculations the potentials developed by Hay and Wadt, and for the MP calculations, the model potentials developed by Sakai and Huzinaga, are employed. © 1992 by John Wiley & Sons, Inc.     

Geometry,basis set,and correlation energy dependence of computed protonation energies of imino bases

The nitrogen protonation energies of the imino bases HN?CHR, where R is H, CH₃, NH₂, OH, and F, have been evaluated to determine the dependence of absolute and relative protonation energies on geometry, basis set, and correlation effects. Reliable absolute protonation energies require a basis set larger than a split-valence plus polarization basis, the inclusion of correlation, and optimized geometries of at least Hartree–Fock 4-31G quality. Consistent relative protonation energies can be obtained at the Hartree–Fock level with smaller basis sets. Extending the split-valence basis set by the addition of polarization functions on all atoms decreases the computed absolute Hartree–Fock nitrogen protonation energies of the imino bases HN?CHR except when R is F, but increases the oxygen protonation energies of the carbonyl bases O?CHR.     

Noble‐Gas Complexes: Theoretical Investigation of Multicenter Polynuclear Species

Ab initio calculations at the MP2 level of theory disclose the conceivable existence of neutral complexes containing four or five distinct noble gases (Ng) each bound to a distinct Be‐atom. These multicenter polynuclear Ng molecules are formally obtained by replacing the H‐atoms of CH₄ and but‐2‐yne with ? NBeNg moieties, which behave as independent monovalent ‘functional groups’. Our investigated complexes include the five homotetranuclear [C(NBeNg)₄] complexes 1 – 5 (Ng=He? Xe), the five heterotetranuclear complexes [CN₄Be₄(He)(Ne)(Ar)(Kr)] ( 6 ), [CN₄Be₄(He)(Ne)(Ar)(Xe)] ( 7 ), [CN₄Be₄(He)(Ne)(Kr)(Xe)] ( 8 ), [CN₄Be₄(He)(Ar)(Kr)(Xe)] ( 9 ), and [CN₄Be₄(Ne)(Ar)(Kr)(Xe)] ( 10 ), and the heteropentanuclear complex [HC₄N₅Be₅(He)(Ne)(Ar)(Kr)(Xe)] ( 11 ). We also investigated the five model complexes [H₃CNBeNg] (Ng=He? Xe) containing a single ? NBeNg moiety. The geometries and vibrational frequencies of all these species, invariably characterized as minimum‐energy structures, were computed at the MP2(full)/6‐31G(d,p)/SDD level of theory, and their stability with respect to the loss of the various Ng‐atoms was evaluated by single‐point calculations at the MP2(full)/6‐311G(d)/SDD level of theory. The beryllium‐Ng binding energies range from ca. 17 (Ng=He) to ca. 63 (Ng=Xe) kJ/mol, and the results of natural‐bond‐orbital (NBO) and atoms‐in‐molecules (AIM) analysis reveal that the Be? Ng interaction is essentially electrostatic for helium, neon, argon, and krypton, and has probably a small covalent contribution for xenon.