Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration

In this study, we synthesized novel α,β-unsaturated 2-cyanoacetamide derivatives (1-5) using microwave-assisted Knoevenagel condensation. Characterization of these compounds was carried out using FTIR and 1H NMR spectroscopy. We then evaluated their in vitro antibacterial activity against both gram-positive and gram-negative pathogenic bacteria. Additionally, we employed in silico methods, including ADMET prediction and density functional theory (DFT) calculations of molecular orbital properties, to investigate these cyanoacetamide derivatives (1-5). Molecular docking was used to assess the binding interactions of these derivatives (1-5) with seven target proteins (5MM8, 4NZZ, 7FEQ, 5NIJ, ITM2, 6SE1, and 5GVZ) and compared them to the reference standard tyrphostin AG99. Notably, derivative 5 exhibited the most favorable binding affinity, with a binding energy of -7.7 kcal mol-1 when interacting with the staphylococcus aureus (PDB:5MM8), while also meeting all drug-likeness criteria. Additionally, molecular dynamics simulations were carried out to evaluate the stability of the interaction between the protein and ligand, utilizing parameters such as Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), Radius of Gyration (Rg), and Principal Component Analysis (PCA). A 50 nanosecond molecular dynamics (MD) simulation was performed to investigate stability further, incorporating RMSD and RMSF analyses on compound 5 within the active binding site of the modeled protein across different temperatures (300, 305, 310, and 320 K). Among these temperatures, compound 5 exhibited an RMSD value ranging from approximately 0.2 to 0.3 nm at 310 K (body temperature) with the 5MM8 target, which differed from the other temperature conditions. The in silico results suggest that compound 5 maintained significant conformational stability throughout the 50 ns simulation period. It is consistent with its low docking energy and in vitro findings concerning α,β-unsaturated cyanoacetamides. Key insights from this study include:•The creation of innovative α,β-unsaturated 2-cyanoacetamide derivatives (1-5) employing cost-effective, licensed, versatile, and efficient software for both in silico and in vitro assessment of antibacterial activity.•Utilization of FTIR and NMR techniques for characterizing compounds 1-5.

Accelerating the discovery of the beyond rule of five compounds that have high affinities toward SARS-CoV-2 spike RBD

The battle against SARS-CoV-2 coronavirus is the focal point for the global pandemic that has affected millions of lives worldwide. The need for effective and selective therapeutics for the treatment of the disease caused by SARS-CoV-2 is critical. Herein, we performed a hierarchical computational approach incorporating molecular docking studies, molecular dynamics simulations, absolute binding energy calculations, and steered molecular dynamics simulations for the discovery of potential compounds with high affinity towards SARS-CoV-2 spike RBD. By leveraging ZINC15 database, a total of 1282 in-clinical and FDA approved drugs were filtered out from nearly 0.5 million protomers of relatively large compounds (MW > 500, and LogP ≤ 5). Our results depict plausible mechanistic aspects related to the blockage of SARS-CoV-2 spike RBD by the top hits discovered. We found that the most promising candidates, namely, ZINC95628821, ZINC95617623, ZINC3979524, and ZINC261494658, strongly bind to the spike RBD and interfere with the human ACE2 receptor. These findings accelerate the rational design of selective inhibitors targeting the spike RBD protein of SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Accelerating the Discovery of the Beyond Rule of Five Compounds That Have High Affinities Toward SARS-CoV-2 Spike RBD.. [DOI: 10.26434/chemrxiv.14130353.v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The battle against SARS-CoV-2 coronavirus is the focal point for the global pandemic that has affected millions of lives worldwide. The need for effective and selective therapeutics for the treatment of the disease caused by SARS-CoV-2 is critical. Herein, we performed computational de novo design incorporating molecular docking studies, molecular dynamics simulations, absolute binding energy calculations, and steered molecular dynamics simulations for the discovery of potential compounds with high affinity towards SARS-CoV-2 spike RBD. By leveraging ZINC15 database, a total of 1282 in-clinical and FDA approved drugs were filtered out from nearly 0.5 million protomers of relatively large compounds (MW > 500, and LogP ≤ 5). Our results depict plausible mechanistic aspects related to the blockage of SARS-CoV-2 spike RBD by the top hits discovered. We found that the most promising candidates, namely, ZINC95628821, ZINC95617623, ZINC3979524, and ZINC261494658, strongly bind to the spike RBD and interfere with the human ACE2 receptor. These findings accelerate the rational design of selective inhibitors targeting the spike RBD protein of SARS-CoV-2.

Accelerating the Discovery of the Beyond Rule of Five Compounds That Have High Affinities Toward SARS-CoV-2 Spike RBD.. [DOI: 10.26434/chemrxiv.14130353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

<div><div><div><p>The battle against SARS-CoV-2 coronavirus is the focal point for the global pandemic that has affected millions of lives worldwide. The need for effective and selective therapeutics for the treatment of the disease caused by SARS-CoV-2 is critical. Herein, we performed computational de novo design incorporating molecular docking studies, molecular dynamics simulations, absolute binding energy calculations, and steered molecular dynamics simulations for the discovery of potential compounds with high affinity towards SARS-CoV-2 spike RBD. By leveraging ZINC15 database, a total of 1282 in-clinical and FDA approved drugs were filtered out from nearly 0.5 million protomers of relatively large compounds (MW > 500, and LogP ≤ 5). Our results depict plausible mechanistic aspects related to the blockage of SARS-CoV-2 spike RBD by the top hits discovered. We found that the most promising candidates, namely, ZINC95628821, ZINC95617623, ZINC3979524, and ZINC261494658, strongly bind to the spike RBD and interfere with the human ACE2 receptor. These findings accelerate the rational design of selective inhibitors targeting the spike RBD protein of SARS-CoV-2.</p></div></div></div>

Accelerating the Discovery of the Beyond Rule of Five Compounds That Have High Affinities Toward SARS-CoV-2 Spike RBD.. [DOI: 10.26434/chemrxiv.14130353.v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The battle against SARS-CoV-2 coronavirus is the focal point for the global pandemic that has affected millions of lives worldwide. The need for effective and selective therapeutics for the treatment of the disease caused by SARS-CoV-2 is critical. Herein, we performed computational de novo design incorporating molecular docking studies, molecular dynamics simulations, absolute binding energy calculations, and steered molecular dynamics simulations for the discovery of potential compounds with high affinity towards SARS-CoV-2 spike RBD. By leveraging ZINC15 database, a total of 1282 in-clinical and FDA approved drugs were filtered out from nearly 0.5 million protomers of relatively large compounds (MW > 500, and LogP ≤ 5). Our results depict plausible mechanistic aspects related to the blockage of SARS-CoV-2 spike RBD by the top hits discovered. We found that the most promising candidates, namely, ZINC95628821, ZINC95617623, and ZINC261494658, strongly bind to the spike RBD and interfere with the human ACE2 receptor. These findings accelerate the rational design of selective inhibitors targeting the spike RBD protein of SARS-CoV-2.

Discovery of potent inhibitors for SARS-CoV-2's main protease by ligand-based/structure-based virtual screening, MD simulations, and binding energy calculations

COVID-19 has caused lockdowns all over the world in early 2020, as a global pandemic. Both theoretical and experimental efforts are seeking to find an effective treatment to suppress the virus. In silico drug design can play a vital role in identifying promising drug candidates against COVID-19. Herein, we focused on the main protease of SARS-CoV-2 that has crucial biological functions in the virus. We performed a ligand-based virtual screening followed by a docking screening for testing approved drugs and bioactive compounds listed in the DrugBank and ChEMBL databases. The top 8 docking results were advanced to all-atom MD simulations to study the relative stability of the protein-ligand interactions. MD simulations support that the catalytic residue, His41, has a neutral side chain with a protonated delta position. An absolute binding energy (ΔG) of -42 kJ mol-1 for the protein-ligand (Mpro-N3) complex has been calculated using the potential-of-mean-force (geometrical) approach. Furthermore, the relative binding energies were computed for the top docking results. Our results suggest several promising approved and bioactive inhibitors of SARS-CoV-2 Mpro as follows: a bioactive compound, ChEMBL275592, which has the best MM/GBSA binding energy; the second-best compound, montelukast, is an approved drug used in the treatment of asthma and allergic rhinitis; the third-best compound, ChEMBL288347, is a bioactive compound. Bromocriptine and saquinavir are other approved drugs that also demonstrate stability in the active site of Mpro, albeit their relative binding energies are low compared to the N3 inhibitor. This study provides useful insights into de novo protein design and novel inhibitor development, which could reduce the cost and time required for the discovery of a potent drug to combat SARS-CoV-2.

High-throughput virtual screening of drug databanks for potential inhibitors of SARS-CoV-2 spike glycoprotein

COVID-19, which is caused by a novel coronavirus known as SARS-CoV-2, has spread rapidly around the world, and it has infected more than 29 million individuals as recorded on 16 September 2020. Much effort has been made to stop the virus from spreading, and there are currently no approved pharmaceutical products to treat COVID-19. Here, we apply an in silico approach to investigate more than 3800 FDA approved drugs on the viral RBD S₁-ACE2 interface as a target. The compounds were investigated through flexible ligand docking, ADME property calculations and protein–ligand interaction maps. Molecular dynamics (MD) simulations were also performed on eleven compounds to study the stability and the interactions of the protein–ligand complexes. The MD simulations show that bagrosin, chidamide, ebastine, indacaterol, regorafenib, salazosulfadimidine, silodosin and tasosartan are relatively stable near the C terminal domain (CTD1) of the S₁ subunit of the viral S protein. The relative MMGBSA binding energies show that silodosin has the best binding to the target. The constant velocity steered molecular dynamics (SMD) simulations show that silodosin preferentially interacts with the RBD S₁ and has potential to act as an interfering compound between viral spike–host ACE2 interactions.

Communicated by Ramaswamy H. Sarma

Computational Design of Potent Inhibitors for SARS-CoV-2’s Main Protease.. [DOI: 10.26434/chemrxiv.12548003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

In silico drug design can play a vital role in identifying promising drug candidates against COVID-19. Herein, we focused on the main protease of SARS-CoV-2 that plays crucial biological functions in the virus. We performed a ligand-based virtual screening followed by a docking screening for testing approved drugs and bioactive compounds listed in the DrugBank and ChEMBL databases. The top 8 docking results were advanced to all-atom MD simulations to study the relative stability of the protein-ligand interactions.Our results suggest several promising approved and bioactive inhibitors of SARS-CoV-2 Mpro.

Computational Design of Potent Inhibitors for SARS-CoV-2’s Main Protease.. [DOI: 10.26434/chemrxiv.12548003.v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

In silico drug design can play a vital role in identifying promising drug candidates against COVID-19. Herein, we focused on the main protease of SARS-CoV-2 that plays crucial biological functions in the virus. We performed a ligand-based virtual screening followed by a docking screening for testing approved drugs and bioactive compounds listed in the DrugBank and ChEMBL databases. The top 8 docking results were advanced to all-atom MD simulations to study the relative stability of the protein-ligand interactions.Our results suggest several promising approved and bioactive inhibitors of SARS-CoV-2 Mpro.

The ozonolysis of cyclic monoterpenes: a computational review

Monoterpenes are prevalent organic compounds emitted to the atmosphere, via biogenic activities in various types of plants. Monoterpenes undergo atmospheric decomposition reactions derived by the potent atmospheric oxidizing agents, OH, O3, and NOx. This review critically surveys literature pertinent to the atmospheric removal of monoterpenes by ozone. In general, the ozonolysis reactions of monoterpenes occur through the so-called Criegee mechanism. These classes of reactions generate a wide array of chemical organic and inorganic low vapor pressure (LVP) species. Carbonyl oxides, commonly known as Criegee intermediates (CIs), are the main intermediates from the gas-phase ozonolysis reaction. Herein, we present mechanistic pathways, reactions rate constants, product profiles, thermodynamic, and kinetic results dictating the ozonolysis reactions of selected monoterpenes (namely carene, camphene, limonene, α-pinene, β-pinene, and sabinene). Furthermore, the unimolecular (vinyl hydroperoxide and ester channels) and bimolecular reactions (cycloaddition, insertion, and radical recombination) of the resulting CIs are fully discussed. The orientations and conformations of the resulting primary ozonides (POZs) and CIs of monoterpenes are classified to reveal their plausible effects on reported thermokinetic parameters.

Comparison of the Standard 6-31G and Binning-Curtiss Basis Sets for Third Row Elements

Ab initio calculations were carried out for isogyric reactions involving the third row elements, Ga, Ge, As, Se, and Br. Geometries of all the reactants and products were optimized at the HF, MP2, and B3LYP levels of theory using the 6-31G(d) and 6-31G(d,p) basis sets. For molecules containing third row elements geometries, frequencies and thermodynamic properties were calculated using both the standard 6-31G and the Binning-Curtiss (BC6-31G) basis sets. In order to determine the performance of these basis sets, the calculated thermodynamic properties were compared to G3MP2 values and where possible to experimental values. Geometries and frequencies calculated with the standard 6-31G and the BC6-31G basis sets were found to differ significantly. Frequencies calculated with the standard 6-31G basis set were generally in better agreement with the experimental values (MAD=40.1 cm(-1) at B3LYP/6-31G(d,p) and 94.2 cm(-1) at MP2/6-31G(d,p) for unscaled frequencies and 29.6 cm(-1) and 24.4 cm(-1), respectively, for scaled frequencies). For all the reactions investigated, the thermodynamic properties calculated with the standard 6-31G basis set were found to consistently be in better agreement with the G3MP2 and the available experimental results. However, the BC6-31G basis set performs poorly for the reactions involving both second and third row elements. Since, in general, the standard 6-31G basis set performs well for all the reactions, we recommend that the standard 6-31G basis set be used for calculations involving third row elements. Using G3MP2 enthalpies of reaction and available experimental heats of formation (ΔHf), previously unknown ΔHf for CH3SeH, SiH3SeH, CH3AsH2, SiH3AsH2, CH3GeH3, and SiH3GeH3 were found to be 18.3, 18.0, 38.4, 82.4, 41.9, and 117.4 kJ mol(-1), respectively.

Computational study on thermochemical properties for perhalogenated methanols (CX3OH) (X = F, Cl, Br)

The perhalogenated methanols (CX3OH; X = F, Cl, and Br) are found in the atmosphere as products of the degradation of halocarbons. The thermochemical properties for these molecules have been calculated at the HF, MP2, and B3LYP levels of theories in conjunction with six different basis sets as well as at G3MP2 and CBS-QB3. Calculated properties include the gas-phase enthalpies of formation (ΔfH(0)), gas-phase acidities (ΔacidG(0)), gas-phase proton affinity, and bond dissociation energies of the C-O and O-H bonds of CX3OH. Excellent agreement is found between the results obtained using G3MP2 and CBS-QB3 methods and the available experimental data. The results obtained using MP2 are more consistent with the experimental, G3MP2, and CBS-QB3 values than those computed at B3LYP. In general, the 6-311+G(d,p) basis set when combined with the HF or MP2 level of theory produced better results than other basis sets considered in this study.

Computational study on the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O

Deamination of adenine is one of several forms of premutagenic lesions occurring in DNA. In the present study, mechanisms for the deamination reaction of adenine with OH−/nH2O (n = 0, 1, 2, 3) and 3H2O were investigated. HF/6-31G(d), B3LYP/6-31G(d), MP2/6-31G(d), and B3LYP/6-31+G(d) levels of theory were employed to search for and optimize all geometries. Energies were calculated at the G3MP2B3 and CBS-QB3 levels of theory. The effect of solvent (water) was computed using the polarizable continuum model (PCM). Intrinsic reaction coordinate (IRC) calculations were performed for all transition states. Five pathways were investigated for the deamination reaction of adenine with OH−/nH2O and 3H2O. The first four pathways (A–D) are initiated by deprotonation at the amino group of adenine by OH−, while pathway E is initiated by tautomerization of adenine. For all pathways the next two steps involve formation of a tetrahedral intermediate followed by dissociation to products via a 1,3-proton shift. Deamination with a single OH− has a high activation barrier (190 kJ mol−1 using the G3MP2B3 level) for the rate-determining step. The addition of one water molecule reduces this barrier by 68 kJ mol−1 at the G3MP2B3 level. Adding additional water molecules decreases the overall activation energy of the reaction, but the effect becomes smaller with each additional water molecule. The most plausible mechanism is pathway E, the deamination reaction of adenine with 3H2O, with an overall G3MP2B3 activation energy of 139 and 137 kJ mol−1 for the gas phase and PCM, respectively. This barrier is lower than that for the deamination with OH−/3H2O by 6 and 2 kJ mol−1 for the gas phase and PCM, respectively.

Theoretical investigation into competing unimolecular reactions encountered in the pyrolysis of acetamide

Motivated by the necessity to understand the pyrolysis of alkylated amines, unimolecular decomposition of acetamide is investigated herein as a model compound. Standard heats of formation, entropies, and heat capacities, are calculated for all products and transition structures using several accurate theoretical levels. The potential energy surface is mapped out for all possible channels encountered in the pyrolysis of acetamide. The formation of acetamedic acid and 1-aminoethenol and their subsequent decomposition pathways are found to afford the two most energetically favored pathways. However, RRKM analysis shows that the fate of acetamedic acid and 1-aminoethenol at all temperatures and pressures is to reisomerize to the parent acetamide. 1-Aminoethenol, in particular, is predicted to be a long-lived species enabling its participation in bimolecular reactions that lead to the formation of the major experimental products. Results presented herein reflect the importance of bimolecular reactions involving acetamide and 1-aminoethenol in building a robust model for the pyrolysis of N-alkylated amides.

Ring-chain equilibria of R-but-3-enoate esters — A quantum mechanical study of direct and indirect ring-closing reactions

Macrocyclic structures can be synthesized through two simultaneous olefin metathesis reactions: either directly through ring-closing metathesis (RCM) or indirectly through an intermediate formed by acyclic diene metathesis (ADMET). The proclivity of a homologous series of 16 R-but-3-enoate esters to form lactones through one of these two processes is studied at the HF/6–31G(d), B3LYP/6–31G(d), and MP2(full)/6–31G(d) levels of theory. Computed Gibbs free energies are used to determine ΔGRCM, ΔGADMET, and ΔΔG (ΔGRCM – ΔGADMET). ΔΔG is evaluated to compare the relative favourability of the RCM and ADMET reactions for the various R-but-3-enoate esters, where each system is differentiated by the number of methylene groups (n) added to the ester chain. When n = 0, 1, 10, or 13, cyclic lactone formation by direct RCM is predicted to be thermodynamically favoured, and the indirect synthesis is preferred for all other heterocyclic structures. The same trend holds between 298.15 and 333.15 K, therefore, the gas-phase model is a reasonable approximation of the experimental reaction conditions. The theoretical model is sufficient for smaller systems, but molecules larger than the n = 6 case do not follow experimental results for similar saturated structures. Hence, the assumptions pertaining to straight-chain and cis-ring conformations need to be re-evaluated. In particular, chain flexibility should be further examined.

Comprehensive study of some well-known molecular numerical integration methods

In a previous study, we compared, both in terms of accuracy and efficiency, the performance of some of the well-known grids, which use the Becke partitioning scheme for molecular numerical integration. We concluded, based on the number of electrons only, that the MultiExp grid performed well compared with the grids proposed by Becke, Gill et al., and Treutler and Ahlrichs. In this work, we re-examine the performance of the same set of grids in addition to the SG-0 grid and a benchmark grid. These grids are evaluated by integrating the Hartree–Fock electron density to calculate the number of electrons, dipole moment, potential energy, and Coulomb repulsion energy. Our results show that, except for the large benchmark grid, none of these grids were completely satisfactory.

SEST: Simulated Electronic Structure Theory

A novel approach to empirically modeling the electronic structure of molecules is introduced. The theory is based on relationships between molecular orbital energy components and the average distance between electrons and electrons and nuclei. The electron-electron and electron-nucleus distances are subsequently related to interatomic distances which provides a means for modeling the electronic structure of molecules. The general energy expression for a simulated electronic structure theory is defined, along with the functional form of the interatomic distance dependent energy functions. The theory is used to model the hydrogen molecule, the first-row hydrides, and ethane. The models, which have the correct RHF/6-31G(d) optimized geometries, also fit the RHF/6-31G(d) energy at equilibrium and the UHF/6-31G(d) energy at the bond dissociation limit as well as some vibrational frequencies.

Properties and applications of the average interparticle distance

The first and second moment operators are used to define the origin invariant shape and size of a molecule or functional group, as well as expressions for the distance between two electrons and the distance between an electron and a nucleus. The measure of molecular size correlates quite well with an existing theoretical measure of molecular volume calculated from isodensity contours. Also, the measure of size is effective in predicting steric effects of substituents which have been measured experimentally. The electron-electron and electron-nuclear distances are related to components of the Hartree-Fock energy. The average distance between two-electrons can model the Coulomb energy quite well, especially in the case of localized molecular orbitals. The average distance between an electron and a nucleus is closely related to the electron-nuclear attraction energy of a molecule.

Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory

Nucleophile (11)C/ (14)C [ k (11)/ k (14)] and secondary alpha-deuterium [( k H/ k D) alpha] kinetic isotope effects (KIEs) were measured for the S N2 reactions between tetrabutylammonium cyanide and ethyl iodide, bromide, chloride, and tosylate in anhydrous DMSO at 20 degrees C to determine whether these isotope effects can be used to determine the structure of S N2 transition states. Interpreting the experimental KIEs in the usual fashion (i.e., that a smaller nucleophile KIE indicates the Nu-C alpha transition state bond is shorter and a smaller ( k H/ k D) alpha is found when the Nu-LG distance in the transition state is shorter) suggests that the transition state is tighter with a slightly shorter NC-C alpha bond and a much shorter C alpha-LG bond when the substrate has a poorer halogen leaving group. Theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion. The results show that the experimental nucleophile (11)C/ (14)C KIEs can be used to determine transition-state structure in different reactions and that the usual method of interpreting these KIEs is correct. The magnitude of the experimental secondary alpha-deuterium KIE is related to the nucleophile-leaving group distance in the S N2 transition state ( R TS) for reactions with a halogen leaving group. Unfortunately, the calculated and experimental ( k H/ k D) alpha's change oppositely with leaving group ability. However, the calculated ( k H/ k D) alpha's duplicate both the trend in the KIE with leaving group ability and the magnitude of the ( k H/ k D) alpha's for the ethyl halide reactions when different scale factors are used for the high and the low energy vibrations. This suggests it is critical that different scaling factors for the low and high energy vibrations be used if one wishes to duplicate experimental ( k H/ k D) alpha's. Finally, neither the experimental nor the theoretical secondary alpha-deuterium KIEs for the ethyl tosylate reaction fit the trend found for the reactions with a halogen leaving group. This presumably is found because of the bulky (sterically hindered) leaving group in the tosylate reaction. From every prospective, the tosylate reaction is too different from the halogen reactions to be compared.

Addition reaction of adamantylideneadamantane with Br2 and 2Br2: a computational study

Ab initio calculations were carried out for the reaction of adamantylideneadamantane (Ad=Ad) with Br2 and 2Br2. Geometries of the reactants, transition states, intermediates, and products were optimized at HF and B3LYP levels of theory using the 6-31G(d) basis set. Energies were also obtained using single point calculations at the MP2/6-31G(d)//HF/6-31G(d), MP2/6-31G(d)//B3LYP/6-31G(d), and B3LYP/6-31+G(d)//B3LYP/6-31G(d) levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. Only one pathway was found for the reaction of Ad=Ad with one Br2 producing a bromonium/bromide ion pair. Three mechanisms for the reaction of Ad=Ad with 2Br2 were found, leading to three different structural forms of the bromonium/Br3- ion pair. Activation energies, free energies, and enthalpies of activation along with the relative stability of products for each reaction pathway were calculated. The reaction of Ad=Ad with 2Br2 was strongly favored over the reaction with only one Br2. According to B3LYP/6-31G(d) and single point calculations at MP2, the most stable bromonium/Br3- ion pair would form spontaneously. The most stable of the three bromonium/Br3- ion pairs has a structure very similar to the observed X-ray structure. Free energies of activation and relative stabilities of reactants and products in CCl4 and CH2ClCH2Cl were also calculated with PCM using the united atom (UA0) cavity model and, in general, results similar to the gas phase were obtained. An optimized structure for the trans-1,2-dibromo product was also found at all levels of theory both in gas phase and in solution, but no transition state leading to the trans-1,2-dibromo product was obtained.

A New Insight into Using Chlorine Leaving Group and Nucleophile Carbon Kinetic Isotope Effects To Determine Substituent Effects on the Structure of SN2 Transition States

Chlorine leaving group k(35)/k(37), nucleophile carbon k(11)/k(14), and secondary alpha-deuterium [(kH/kD)alpha] kinetic isotope effects (KIEs) have been measured for the SN2 reactions between para-substituted benzyl chlorides and tetrabutylammonium cyanide in tetrahydrofuran at 20 degrees C to determine whether these isotope effects can be used to determine the substituent effect on the structure of the transition state. The secondary alpha-deuterium KIEs indicate that the transition states for these reactions are unsymmetric. The theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion; i.e., they suggest that the transition states for these reactions are unsymmetric with a long NC-C(alpha) and reasonably short C(alpha)-Cl bonds. The chlorine isotope effects suggest that these KIEs can be used to determine the substituent effects on transition state structure with the KIE decreasing when a more electron-withdrawing para-substituent is present. This conclusion is supported by theoretical calculations. The nucleophile carbon k(11)/k(14) KIEs for these reactions, however, do not change significantly with substituent and, therefore, do not appear to be useful for determining how the NC-C(alpha) transition-state bond changes with substituent. The theoretical calculations indicate that the NC-C(alpha) bond also shortens as a more electron-withdrawing substituent is placed on the benzene ring of the substrate but that the changes in the NC-C(alpha) transition-state bond with substituent are very small and may not be measurable. The results also show that using leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is more complicated than previously thought. The implication of using both chlorine leaving group and nucleophile carbon KIEs to determine the substituent effect on transition-state structure is discussed.

Quantum mechanical size and steric hindrance

A quantum mechanical definition of molecular size and shape is formulated from the electronic second moment of the Hartree-Fock wave function. The shape tensor is defined to be invariant with respect to the origin. The geometric average of the eigenvalues of the tensor correlates very well with van der Waals and Bragg-Slater radii. There is also a close linear relationship between this definition of molecular size and molecular volumes determined computationally using isodensity contours. Furthermore, this definition of molecular size is effective in predicting the steric effects of substituents, as predicted by existing methods, such as the modified Taft Ee(s), P-values, and n-values.

Computational Study of the Reactions of SiH3X (X = H, Cl, Br, I) with HCN

Ab initio calculations were carried out for the reactions of silane and halosilanes (SiH3X, X=H, Cl, Br, I) with HCN. Geometries of the reactants, transition states, intermediates and products were optimized at HF, MP2, and B3LYP levels of theory using the 6-31G(d) and 6-31G(d,p) basis sets. Energies were also obtained using G3MP2 and G3B3 levels of theory. Intrinsic reaction coordinate (IRC) calculations were performed to characterize the transition states on the potential energy surface. It was found that HCN can react with silane and halosilanes via three different mechanisms. One involves HX elimination by a one-step pathway producing SiH3CN. The second mechanism consists of H2 elimination, producing SiH2XCN via a one-step pathway or three multiple-step pathways. The third mechanism involves dissociation of SiH3X to various products, which can then react with HCN. Activation energies, enthalpies, and free energies of activation along with the thermodynamic properties (DeltaE, DeltaH, and DeltaG) of each reaction pathway were calculated. The reaction of SiH3X with HCN produce different products depending on substituent X. We have found that the standard 6-31G(d) bromine basis set gave results which were in better agreement with the G3MP2 results than for the Binning-Curtiss basis set. Computed heats of formation (DeltaHf) for SiH3CN, SiH3NC, SiH2ClCN, SiH2BrCN, SiH2ICN, SiHCl, SiHBr, and SiHI were found to be 133.5, 150.8, -34.4, 23.6, 102.4, 48.7, 127.1, and 179.8 kJ mol-1, respectively. From enthalpies calculated at G3MP2, we predict that the DeltaHf for SiH2 to be 262.8 kJ mol-1 compared to the experimental value of 273.8+/-4.2 kJ mol-1.

Computational Study of the Deamination Reaction of Cytosine with H2O and OH-

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.

Ab initio study of the decomposition of formamidine

The decomposition of formamidine yielding hydrogen cyanide and ammonia has been investigated by ab initio calculations. Optimized geometries for reactants, transition states, and products were determined at the HF/6-31G(d) and MP2/6-31G(d) levels of theory. Energies were also determined at the G1, G2, G2MP2, G3, G3B3, G3MP2, and G3MP2B3 levels of theory. The role of water in the decomposition reaction of formamidine was examined. Intrinsic reaction coordinate (IRC) analysis was carried out for all transition states. Activation energies, enthalpies and free energies of activation were also calculated for each reaction pathway. G3 level of theory predicts the gas-phase decomposition of formamidine to have a high activation energy of 259.1 kJ mol–1. Adding one water molecule catalyses the reaction by forming a cyclic hydrogen-bonded transition state, reducing the barrier to 169.4 kJ mol–1 at the G3 level. Addition of a second water, which acts as a "solvent" molecule, further reduces the barrier to 151.1 kJ mol–1 at the G3 level. These values are still high and explain why rather extreme conditions are necessary to achieve this reaction experimentally. Thermodynamic properties (ΔE, ΔH, and ΔG) for each reaction pathway studied were also calculated. The G3 heats of reaction (ΔE) of the gas-phase decomposition of formamidine, its complex with one water molecule, and its complex with two water molecules are 0.9, 2.2, and –5.1 kJ mol –1, respectively. The G3 heat of reaction for the gas-phase decomposition to yield separated products is 22.3 kJ mol–1. Free energies of reaction and of activation in aqueous solution were calculated with PCM using the KLAMT cavity model. At MP2 the formamidine reaction is found to be exergonic in aqueous solution and to favour formation of the separated products (NH3 + HCN). The solvent model predicts a significant lowering of the free energy of activation (16–18 kJ mol–1) for the unimolecular reaction and 21–42 kJ mol–1 for the water-mediated reaction in aqueous solution relative to the gas phase. Key words: decomposition reaction, formamidine, Hartree–Fock, post Hartree–Fock, Gaussian-n theories, IRC, solvation models, PCM, KLAMT.

An ab initio study of 1,5-suprafacial shifts in 5-substituted 1,3-cyclopentadienes

A computational study of the degenerate 1,5-suprafacial migration of the 5-substituted cyclopentadienes is presented. The substituents considered are the Group 14–17 elements of the second through fifth periods, saturated by hydrogens as needed to fulfill normal valence requirements. The geometry of most transition states are remarkably similar in the carbon framework. The activation barrier to migration was shown to correlate well with a dimensionless "stretching" parameter, especially at the MP2 level.Key words: 5-substituted 1,3-cyclopentadiene, 1,2-haptotropic shift, 1,5-suprafacial shift, ab initio, transition states.

Exo selectivity and the effect of disubstitution in the Diels–Alder reactions of butadiene with 3,3-disubstituted cyclopropenes

A density functional computational study was performed to accomplish two tasks: to examine the endo–exo selectivity in the Diels–Alder reactions of 3,3-disubstituted cyclopropenes with s-cis-butadiene, and to study the effect of disubstitution on the reactivity of the cyclopropene dienophile. Cyclopropene is substituted at C-3 with CH3, SiH3, NH2, PH2, OH, SH, F, and Cl; both 3-substituted and 3,3-disubstituted ground states are examined to determine relative reactivities. The exo transition-state structures are consistently lower in energy than the endo transition-state structures for the 3,3-disubstituted cyclopropene – butadiene system, and surprisingly, both modes of addition have lower activation barriers than the syn 3-substituted cyclopropene – butadiene system. Through a series of isodesmic reactions, we have concluded that there is an additional stabilization in the transition-state structures of the 3,3-disubstituted system that can account for the lowering of the activation barriers below that of the 3-substituted cases. This stabilization is a combination of the anomeric effect and the ring relaxation that occurs in the transition-state structure.Key words: Diels–Alder reaction, cyclopropene, exo selectivity, anomeric effect.