Theoretical studies on pteridines. 2. Geometries,tautomer, ionization and reduction energies of substrates and inhibitors of dihydrofolate reductase

Ab initio SCF calculations with STO-3G and 3-21G basis sets are reported for approximately 85 pteridines of interest to the study of the reaction and inhibition mechanisms of dihydrofolate reductase. These include tautomeric, protonated, deprotonated, reduced and 6-substituted forms of the 2-amino-4-oxo- and 2,4-diamino-pteridines, many of which are not easily amenable to experimental investigation. Full geometry optimizations at the SCF/STO-3G level for 30 such pteridines have been performed. A step-wise computational protocol designed to identify the minimum level of theory necessary for reliable prediction of relative tautomer, reduction and ionization energies has been developed in an effort to minimize the cost of calculations for this reasonably large N-heterobicylic system. In general, SCF/STO-3G results were found to be inadequate while SCF/3-21G results obtained with STO-3G optimized geometries agreed with all available experimental evidence with the exception of the relative acidity of 6-methyl-7,8-dihydropterin. Correlation graphs relating experimental pK_a's to the calculated ionization energies are presented: these are of potential predictive value. An analysis is given of the importance of resonance substructures, such as the guanidinium and extended-guanidinium groups, in stabilizing some preferred tautomeric and ionized forms, and in explaining the observed geometry changes.     

Towards understanding the origins of the different specificities of binding the reduced (NADPH) and oxidised (NADP+) forms of nicotinamide adenine dinucleotide phosphate coenzyme to dihydrofolate reductase

Lactobacillus casei dihydrofolate reductase (DHFR) binds more than a thousand times tighter to NADPH than to NADP⁺. The origins of the difference in binding affinity to DHFR between NADPH and NADP⁺ are investigated in the present study using experimental NMR data and hybrid density functional, B3LYP, calculations. Certain protein residues (Ala 6, Gln 7, Ile 13 and Gly 14) that are directly involved in hydrogen bonding with the nicotinamide carboxamide group show consistent differences in ¹H and ¹⁵N chemical shift between NADPH and NADP⁺ in a variety of ternary complexes. B3LYP calculations in model systems of protein-coenzyme interactions show differences in the H-bond geometry and differences in charge distribution between the oxidised and reduced forms of the nicotinamide ring. GIAO isotropic nuclear shieldings calculated for nuclei in these systems reproduce the experimentally observed trends in magnitudes and signs of the chemical shifts. The experimentally observed reduction in binding of NADP⁺ compared with NADPH results partly from NADP⁺ having to change its nicotinamide amide group from a cis- to a trans-conformation on binding and partly from the oxidised nicotinamide ring of NADP⁺ being unable to take up its optimal hydrogen bonding geometry in its interactions with protein residues.     

Conformational analysis,part 43. A theoretical and LIS/NMR investigation of the conformations of substituted benzamides

A refined Lanthanide‐Induced‐Shift Analysis (LISA) is used with molecular mechanics and ab initio calculations to investigate the conformations of benzamide ( 1 ), N‐methylbenzamide ( 2 ), N,N‐dimethylbenzamide ( 3 ) and the conformational equilibria of 2‐fluoro ( 4 ), 2‐chloro ( 5 ) and N‐methyl‐2‐methoxy benzamide ( 6 ). The amino group in 1 is planar in the crystal but is calculated to be pyramidal with the CO/phenyl torsional angle (ω) of 20–25°. The LISA analysis gave acceptable agreement factors (Rcryst ≤ 1%) for the ab initio geometries when ω was decreased to 0°, the other geometries were not as good. In 2 , the N‐methyl is coplanar with the carbonyl group in all the geometries. Good agreement was obtained for the RHF geometries, with ω 25°, the other geometries were only acceptable with increased values of ω. In 3 , good agreement for the RHF and PCModel geometries was found when ω was changed from the calculated values of 40° (RHF) and 90° (PCModel) to ca. 60°, the X‐ray and B3LYP geometries were not as good. The two substituted compounds 4 , 5 and 6 are interconverting between the cis (O,X) and trans (O,X) conformers. The more stable trans conformer is planar in 4 and 6 but the cis form non‐planar. Both the cis and trans conformers of 5 are non‐planar. There is an additional degree of freedom in 6 due to the 2‐methoxy group, which can be either planar or orthogonal to the phenyl ring in both conformers. The conformer ratios were obtained from the LISA analysis to give Ecis‐Etrans in 4 > 2.3 kcal/mol (CDCl₃) and 1.7 kcal/mol (CD₃CN), in 5 0.0 kcal/mol (CD₃CN) and in 6 > 2.5 kcal/mol (CDCl₃) and 2.0 kcal/mol (CD₃CN). These values were used with the observed versus calculated ¹H shifts to determine the conformer ratios and energies in DMSO solvent to give Ecis‐Etrans 1.1, ?0.1 and 1.8 kcal/mol for ( 4 ), ( 5 ) and ( 6 ). Comparison of the observed versus calculated conformer energies show that both the MM and ab initio calculations overestimate the NH..F hydrogen bond in ( 4 ) by ca. 2 kcal/mol. Copyright © 2015 John Wiley & Sons, Ltd.     

Computational study of sulfoxides of thiacyclohexane, 4‐silathiacyclohexane, 4‐fluoro‐4‐silathiacyclohexane,and 4,4‐difluoro‐4‐silathiacyclohexane: Relative energies of conformations and sulfinyl oxygen stabilized pentacoordinate silicon in boat and twist structures

Second‐order Møller‐Plesset theory (MP2) has been used to calculate the equilibrium geometries and relative energies of the chair, 1,4‐twist, 2,5‐twist, 1,4‐boat, and 2,5‐boat conformations of thiacyclohexane 1‐oxide (tetrahydro‐2H‐thiopyran 1‐oxide), 4‐silathiacyclohexane 1‐oxide, cis‐ and trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide, and 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide. At the MP2/6‐311+G(d,p) level of theory, the chair conformer of axial thiacyclohexane 1‐oxide is 0.99, 5.61, 5.91, 8.57, and 7.43 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 2,5‐twist conformers and 1,4‐boat and 2,5‐boat transition states. The chair conformer of equatorial thiacyclohexane 1‐oxide is 4.62, 6.31, 7.56, and 7.26 kcal/mol more stable (ΔE) than its respective 1,4‐twist and 2,5‐twist conformers and 1,4‐boat and 2,5‐boat transition states. The chair conformer of axial 4‐silathiacyclohexane 1‐oxide is 1.79, 4.26, 3.85, and 5.71 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 2,5‐twist conformers and 2,5‐boat transition state. The 2,5‐twist conformer of axial 4‐silathiacyclohexane 1‐oxide is stabilized by a transannular interaction between the sulfinyl oxygen and silicon, to give trigonal bipyramidal geometry at silicon. The chair conformer of equatorial 4‐silathiacyclohexane 1‐oxide is 2.47, 7.90, and 8.09 kcal/mol more stable (ΔE) than its respective 1,4‐twist, and 2,5‐twist conformers and 2,5‐boat transition state. The chair conformer of axial cis‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide is 4.18 and 5.70 kcal/mol more stable than its 1,4‐twist conformer and 2,5‐boat transition state and 1.51 kcal/mol more stable than the chair conformer of equatorial cis‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide. The chair conformer of axial trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide is 5.02 and 6.11 kcal/mol more stable than its respective 1,4‐twist conformer and 2,5‐boat transition state, but is less stable than its 2,5‐twist conformer (ΔE = ?1.77 kcal/mol) and 1,4‐boat transition state (ΔE = ?1.65 kcal/mol). The 2,5‐twist conformer and 1,4‐boat conformer of axial trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide are stabilized by intramolecular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The chair conformer of axial 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide is 3.02, 5.16, 0.90, and 6.21 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 1,4‐boat conformers and 2,5‐boat transition state. The 1,4‐boat conformer of axial 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide is stabilized by a transannular coordination of the sulfinyl oxygen with silicon that results in a trigonal bipyramidal geometry at silicon. The relative energies of the conformers and transition states are discussed in terms of hyperconjugation, orbital interactions, nonbonded interactions, and intramolecular sulfinyl oxygen–silicon coordination. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

Two conformers of protonated pyruvate, CH₃C⁺(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C? C? C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C? COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH₃COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C? COO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C? C? O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ? OC hydrogen bond. © 1993 John Wiley & Sons, Inc.     

Relative stability,potential barrier and intensity parameters of the trans and cis isomers of fluoroacetyl fluoride: An ab initio study

Ab initio calculations have been performed to determine molecular geometries, relative stabilities and the potential barrier of the fluoroacetyl fluoride molecule. The calculations indicate the existence of two stable conformations, trans and cis, in agreement with experimental studies. The potential barrier presents a maximum around 80° and an energy difference of ⋍ 17.5 kJ mol⁻¹ with respect to the most stable conformer (trans). These calculations also confirm that this conformer is more polar than the cis form, with the total dipole moment oriented along the carbonylic bond. The intensity parameters of the trans and cis isomers in terms of their atomic polar tensors have been analysed using the “charge-charge flux-overlap” model. The calculations predict similar atomic polar tensors for both forms, suggesting practically equivalent electronic structures in the ground state.     

Synthesis and transformations of stereoisomeric ethyl 2‐isothiocyanato‐1‐cyclopentanecarboxylatesm

Ethyl vis‐ and trans‐2‐isothiocyanato‐1‐cyclopentanecarboxylates 2 and 7 were prepared by the reaction of the corresponding alicyclic ethyl 2‐amino‐1‐carboxylates and thiophosgene. The cis‐isothiocyanato compound 2 underwent ring closure with amines in one or two steps, resulting in 3‐substituted‐cis‐2‐thioxocyclopenta[d]pyrimidin‐4‐ones 3a‐g. The trans isomer 7 failed to cyclize, but gave carboxamide 8a,b or thiourea ester derivatives 9a,b.     

Light activates reduction of methotrexate by NADPH in the ternary complex with Escherichia coli dihydrofolate reductase

Methotrexate (MTX), a strong inhibitor of dihydrofolate reductase (DHFR), has been widely used for chemotherapy for many types of cancer as well as for juvenile rheumatoid arthritis. It mimics folate substrates and binds tightly to the active site of DHFR, perhaps in a conformation close to the transition state of the folate catalyzed reaction. Absorption, fluorescence and ultrasensitive Raman difference spectroscopies show that light-activated MTX reacts with NADPH in the enzyme active site, producing 5,8-dihydromethotrexate (5,8-dihydro-MTX) and NADP+. The reaction, which proceeds with a hydride transfer between C4 (pro-R side) of the nicotinamide ring and N5 of the pteridine ring, is similar to that between folate and NADPH except that the hydride is transferred to C6 in this case. Hence, MTX is catalytically competent in its excited state. Most experiments were performed on the Escherichia coli enzyme, but preliminary studies show that the reaction also occurs with human DHFR.     

Theoretical study of the barriers to internal rotation in nitrous acid

Nitrous acid, HONO, has been studied for three geometries by the ab initio LCAO SCF MO method with a basis of accurate gaussian atomic orbitals. The trans geometry is correctly predicted to be most stable, lying about 2 kcal/mole lower than the cis form, and 9 kcal/mole lower than the 90° form (experimental estimates being 0.4 and 11.6 kcal/mole, respectively). Population analysis, dipole moment components, and properties related to nuclear-nuclear and nuclear-electron potentials all show a partial breaking of the hydroxyl oxygen-nitrogen bond at 90° compared to cis and trans, as well as the effects of electronic rearrangement for nuclear screening in the high nuclear repulsion cis form. The cis to 90° barrier is dominated by the attractive components of the total energy, while the trans to 90° one is dominated by repulsive components, in agreement with our analysis and an earlier prediction by Allen.     

Steric as well as n→π* Interaction Controls the Conformational Preferences of Phenyl Acetate: Gas‐phase Spectroscopy and Quantum Chemical Calculations

Herein, we report that the conformational preference of phenyl acetate is governed by steric effect and n→π* interaction. Conformation‐specific electronic and IR spectroscopy combined with quantum chemistry calculations confirm the presence of only the cis conformer of phenyl acetate in the experiment. The cis conformer of phenyl acetate has n→π* interaction between the lone‐pair electrons on the carbonyl oxygen atom and the π* orbitals of the phenyl group. The n→π* interaction is absent in the trans conformer which has additional steric repulsion between the methyl group and phenyl ring. The trans conformer is higher in energy than the cis conformer by ≈3 kcal mol^?1. We have found the effect of methyl substitution on the strength of the n→π* interaction, steric repulsion, and hyperconjugation in phenyl acetate. The red‐shift observed in the cis conformer of phenyl acetate with respect to the trans conformer is affected due to the influence of the methyl substituent on the strength of the n→π* interaction as well as hyperconjugation. The present result demonstrates that the introduction of a bulkier substituent can induce steric as well as electronic control to reduce conformational heterogeneity of a molecular system. Understanding the effect of bulkier substituents to promote defined conformations having specific non‐covalent interactions may have implication in better perception of the optimum structure and function of biomolecules as well as recognition of drugs by biomolecules.     

The cis-trans Isomerisation of Homologous 2-Hydroxycycloalkanecarboxylic Acids under Basic Conditions

The cis→trans isomerisation of homologous 2-hydroxycycloalkanecarboxylic acids in strongly basic aqueous solution was studied starting from the cis isomers. It was found that the cyclopentane, cyclohexane and cycloheptane homologues afforded synthetically useful amounts of the trans acids and the procedure resulted in relatively small quantities of the corresponding olefinic acids. In contrast, the isomerisation of the cis-2-hydroxycyclooctanecarboxylic acid produced roughly equal amounts of the cis and trans isomers and the 1-cyclooctenecarboxylic acid at equilibrium. Molecular modelling with the PM3 semiempirical method of the reactants, products and the intermediates applying explicit water molecules as reaction medium gave a fair estimate for the rate sequence of the idealised （dehydration-free） isomerisation reactions in aqueous base solution.     

Low-temperature 15N NMR spectra of reduced 1,3-heterocyclic systems

The ¹⁵N NMR spectra of the O-inside cis-fused conformer of perhydropyrido[1,2-c][1,3]thiazine shows a shielding of the nitrogen of 23.0 ppm relative to the trans-fused conformer. In contrast, ¹⁵N shifts for the cis-and trans-fused conformers of perhydro-oxazolo[3,4-a]pyridine and perhydrothiazolo[3,4-a]pyridine show corresponding shieldings of only 0.6 and 2.5 ppm, respectively.     

Regioselective synthesis of cis- and trans-2,4,5-triarylimidazolines and 2,4,5-triarylimidazoles from available reagents

Novel data were obtained concerning the reaction of aromatic aldehydes with ammonia. A preparative method for the synthesis of new substituted 1,3,5-triaryl-2,4-diazapenta-1,4-dienes was developed. These products are the starting reactants for syntheses of cis- and trans-2,4,5-triaryl-2-imidazolines and 2,4,5-triarylimidazoles.     

Compounds with bridgehead nitrogen. 44—the conformational analysis of perhydropyrido[1,2-c] [1,3]thiazine

The 270 MHz NMR data on trans- and cis-(H-4a, H-7)-7-ethylperhydropyrido[1,2-c][1,3]thiazine show heavy conformational bias to the trans- and S-inside cis-fused conformations, respectively. Comparison of the ¹³C NMR spectra of these anancomeric systems with the ¹³C NMR spectrum of perhydropyrido[1,2-c][1,3]thiazine indicates a trans-?S-inside cis-conformational equilibrium for the latter compound in CDCl₃ at 25°C, containing ca 75% trans-fused conformer. The ¹³C NMR spectrum of perhydropyrido[1,2-c][1,3]-thiazine at ?75°C showed 64% trans-fused conformer and 36% S-inside cis-conformer.     

Conformational analysis,barriers to internal rotation,ab initio calculations and vibrational assignment of fluoroacetone

The infrared (3500-20 cm⁻¹) and Raman (3200-10 cm⁻¹) spectra have been recorded for gaseous and solid fluoroacetone (1-fluoro-2-propanone), CH₂FC(O)CH₃. Additionally, the Raman spectrum of the liquid has been recorded and qualitative depolarization values have been obtained. These data have been interpreted on the basis that the molecule exists predominantly in the cis (fluorine atom oriented cis to the methyl group) conformation in the vapor but for the liquid a second conformer having a trans orientation (fluorine atom oriented trans to the methyl group) is present. From a study of the Raman spectrum of the liquid at variable temperatures the trans conformation has been determined to be more stable than the cis form by 416 ± 54 cm⁻¹ (1.19 ± 0.15 kcal mol⁻¹) and is the only conformation present in the spectrum of the annealed solid. The asymmetric torsional fundamental for the more stable cis conformer has been observed in the far infrared spectrum of the gas at 69.6 cm⁻¹ with six accompanying hot band transitions proceeding to lower frequency. The corresponding mode for the high energy trans conformer is extensively overlapped but is distinguishable at ∼65 cm⁻¹. From these data the asymmetric torsional potential function governing internal rotation about the CC bond has been determined and the potential coefficients are: V₁ = 675 ± 2, V₂ = 991 ± 5, V₃ = 74 ± 1 and V₄ = 54 ± 2 cm⁻¹. The cis to trans and trans to cis barriers are 1332 ± 5 and 731 ± 5 cm⁻¹, respectively, with an enthalpy difference of 601 ± 8 cm⁻¹ (1.72 ± 0.02 kcal mol⁻¹). From ab initio calculations at the 3-21G and 6-31G* basis set levels optimized geometries for both the cis and trans conformers have been obtained and the potential surface governing internal rotation of the asymmetric top determined. The observed vibrational frequencies with their assignments for both the cis and trans conformers are compared to those from the ab initio calculations. All of these results are compared to the corresponding quantities for some similar molecules.     

All-electron SCF LCAO MO calculations on various conformations of cis- and trans-stilbene

Ab initio SCF calculations of cis- and trans-stilbene at different conformations were performed using two program systems. Minimal energy is obtained for cis-stilbene when the phenyl rings are rotated by 52 ° out of the molecular plane. The deviation from planarity due to steric hindrance is smaller for the trans isomer yielding a rotational angle of 19 °. The trans isomer is calculated to be more stable by 5.7 kcal/mole than the cis isomer, confirming the experimental estimate according to which the energy of isomerization is about 3 kcal/mole. This is an improvement over semiempirical calculations which predict a lower energy for the trans configuration.     

Internal Rotation of Ester Linkage in Phenyl Benzoate and Hydroxybenzoic Acid Dimer as Models of Aromatic Polyesters Using Density Functional Theory

The internal rotation of the ester linkage was reinvestigated more quantitatively by using the density functional theory (DFT) in order to understand the characteristic stiffness and extendedness of polymer chain found in aromatic polyesters. Phenyl benzoate ( PB ) and p‐hydroxybenzoic acid (HBA) dimer ( HB ) were selected as models of aromatic polyesters. The relaxed potential energy surface (PES) scan was carried out along the internal rotation of three bonds (denoted as R, S and T, respectively) of the aromatic esters by using the hybrid DFT (B3LYP) with 6‐31G* basis set. The rotation of S bond, which mainly determines the linearity of the molecule, leads to the trans‐ and cis‐conformers of PB . Since the cis‐conformer of PB is 7.69 kcal·mol^–1 higher than the trans‐conformer, the cis‐conformer has little population at standard condition. HB does not have the cis‐conformer. In addition, the chain persistence length of 364 Å is obtained by the rotation matrix formalism using the structural parameters of HB . These agree with the experimental understanding that poly(p‐hydroxybenzoic acid) is the class of stiff and extended polymer.     

Computational studies of 1,2-dithiete and dithioglyoxal

Ab initio calculations are reported on the energies, geometries, vibrational frequencies, and ionization potentials of the H₂C₂S₂ isomers: 1,2-dithiete, cis-dithioglyoxal, and trans-dithioglyoxal. In contrast to most earlier computations, the results of this work indicate that 1,2-dithiete and cis-dithioglyoxal lie close in energy (within 3 kcal/mol) with the dithial more stable. Trans-dithioglyoxal is found to be 4.1 kcal/mol more stable than the cis isomer and faces a barrier to internal rotation of 5.5 kcal/mol. The predicted rotational constants for 1,2-dithiete agree within ～0.05 GHz with the experimentally observed values thus lending credence to the predictions for cis-dithioglyoxal (A_e 14.30683, B_e 2.46324, C_e 2.10143 GHz). Vibrational frequencies are given as potential aids to the identification of these molecules. 6-31G* ΔSCF calculations predict that at low energies (8 to 13 eV) the photoelectron spectra of 1,2-dithiete, cis-dithioglyoxal and trans-dithioglyoxal should be similar.     

Equilibres conformationnels de dérivés de sucres à insaturation terminale

The conformation in solution of several unsatured sugars of the general type XHC?CH—glycosyl has been studied by NMR. In the trans series, the population of the sterically permitted gauche conformer increases with the M-ability of X. In the cis series, the population of the trans conformer increases with the space requirements of X. These phenomena are discussed.     

Theoretical study of thermal decomposition of azomethane

Summary.  Thermal one- and two-bond dissociation processes of cis- and trans-azomethane were studied by ab initio computation with DZP and TZ2P basis sets, using the d(N–C) bond lengths as the reaction coordinates. The geometries were optimized at the MP2 level, and the dissociation energies obtained exploiting a single-point, fourth-order M?ller–Plesset calculations [MP4SDTQ/TZ2P]. At this level of theory including zero-point energies, the trans-isomer is by 9.3 kcal/mol more stable than the cis-isomer. The results show that the energetically more favourable one-bond cleavage proceeds without transition state with the predicted bond dissociation energy D ₀ of 47.8 kcal/mol for trans-azomethane and 38.5 kcal/mol for cis-azomethane. With calculated barrier heights the unimolecular dissociation rate constants have been determined by means of the RRKM theory. The second-order saddle points localized for synchronous decomposition pathways lie 13 (trans)-23(cis) kcal/mol above the one-bond dissociation energies [MP2/DZP]. Received May 28, 1996/Final version received November 1, 1996 / Accepted November 1, 1996