Non-enzymatic and enzymatic hydrolysis of alkyl halides: A haloalkane dehalogenation enzyme evolved to stabilize the gas-phase transition state of an SN2 displacement reaction

The semiempirical PM3 method, calibrated against ab initio HF/6–31+G(d) theory, has been used to elucidate the reaction of 1,2-dichloroethane (DCE) with the carboxylate of Asp-124 at the active site of haloalkane dehalogenase of Xanthobacter autothropicus. Asp-124 and 13 other amino acid side chains that make up the active site cavity (Glu-56, Trp-125, Phe-128, Phe-172, Trp-175, Leu-179, Val-219, Phe-222, Pro-223, Val-226, Leu-262, Leu-263, and His-289) were included in the calculations. The three most significant observations of the present study are that: (i) the DCE substrate and Asp-124 carboxylate, in the reactive ES complex, are present as an ion-molecule complex with a structure similar to that seen in the gas-phase reaction of AcO− with DCE; (ii) the structures of the transition states in the gas-phase and enzymatic reaction are much the same where the structure formed at the active site is somewhat exploded; and (iii) the enthalpies in going from ground states to transition states in the enzymatic and gas-phase reactions differ by only a couple kcal/mol. The dehalogenase derives its catalytic power from: (i) bringing the electrophile and nucleophile together in a low-dielectric environment in an orientation that allows the reaction to occur without much structural reorganization; (ii) desolvation; and (iii) stabilizing the leaving chloride anion by Trp-125 and Trp-175 through hydrogen bonding.

Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7

We investigated the relative free energies of hapten binding to the germ line and mature forms of the 48G7 antibody Fab fragments by applying a continuum model to structures sampled from molecular dynamics simulations in explicit solvent. Reasonable absolute and very good relative free energies were obtained. As a result of nine somatic mutations that do not contact the hapten, the affinity-matured antibody binds the hapten >104 tighter than the germ line antibody. Energetic analysis reveals that van der Waals interactions and nonpolar contributions to solvation are similar and drive the formations of both the germ line and mature antibody–hapten complexes. Affinity maturation of the 48G7 antibody therefore appears to occur through reorganization of the combining site geometry in a manner that optimizes the balance of gaining favorable electrostatic interactions with the hapten and losing those with solvent during the binding process. As reflected by lower rms fluctuations in the antibody–hapten complex, the mature complex undergoes more restricted fluctuations than the germ line complex. The dramatically increased affinity of the 48G7 antibody over its germ line precursor is thus made possible by electrostatic optimization.

Molecular mechanics calculations of the riboacetal internucleotide linkage in double and triple helices.

Structures of Watson-Crick base paired 15-nucleobase oligomer strands in A-type or B-type conformation in which one strand [a strand of alternating nucleotide and riboacetal thymidine nucleoside (RT) units, RP] is DNA and the other is composed of alternating nucleotides and riboacetal nucleosides have been studied by molecular mechanics. Analogously, oligomer strands of RNA in place of DNA have been modeled. The calculations indicate that the RP strand is more stable when complexed in an A-type duplex relative to a B-type form and that this conformational preference is presumably due to the more uniform nature of the former. Nearly planar ribose rings were more commonly observed in the minimized structures of the B-type DNA.RP duplexes as compared with A-type duplexes, despite the fact that planar ribofuranose rings are known to be energetically unfavorable in oligonucleotides. Computed relative stabilities of all duplexes containing the RP strand suggest that such heteroduplexes are less stable than the corresponding double-stranded DNA and double-stranded RNA species. These findings are in agreement with experimental results which show, when equivalent sequences were compared, that a DNA.RNA control forms a more stable duplex than RP hound to a complementary single-stranded RNA strand. In contrast, molecular mechanics studies of complementary triple-helical (DNA)2.RP, (DNA)2.DNA, and (DNA)2.RNA structures indicate that the binding of RP as a Hoogsteen strand stabilizes the underlying duplex to a greater extent compared with native oligonucleotides. These calculations suggest that puckering of the ribose ring in the riboacetal linkage leads to a more favorable interaction with a complementary nucleic acid target than the proposed planar geometry and that this puckering may account for the enhanced binding of RP to a double-stranded target.

Some examples of modeling in chemical engineering: thermal treatment of polymers, phase equilibrium calculations and process design

Presentation submitted to PSE Seminar, Chemical Engineering Department, Center for Advanced Process Design-making (CAPD), Carnegie Mellon University, Pittsburgh (USA), October 2012.

Emergence of half-metallicity in suspended NiO chains: Ab initio electronic structure and quantum transport calculations

Contrary to the antiferromagnetic and insulating character of bulk NiO, one-dimensional chains of this material can become half metallic due to the lower coordination of their atoms. Here we present ab initio electronic structure and quantum transport calculations of ideal infinitely long NiO chains and of more realistic short ones suspended between Ni electrodes. While infinite chains are insulating, short suspended chains are half-metallic minority-spin conductors that displays very large magnetoresistance and a spin-valve behavior controlled by a single atom.

Improvements in DFT Calculations of Spin–Spin Coupling Constants

Different types of spin–spin coupling constants (SSCCs) for several representative small molecules are evaluated and analyzed using a combination of 10 exchange functionals with 12 correlation functionals. For comparison, calculations performed using MCSCF, SOPPA, other common DFT methods, and also experimental data are considered. A detailed study of the percentage of Hartree–Fock exchange energy in SSCCs and in its four contributions is carried out. From the above analysis, a combined functional formed with local Slater (34%), Hartree–Fock exchange (66%), and P86 correlation functional (S66P86) is proposed in this paper. The accuracy of the values obtained with this hybrid functional (mean absolute deviation of 4.5 Hz) is similar to that of the SOPPA method (mean absolute deviation of 4.6 Hz).

Cleavage of the C–C Bond in the Ethanol Oxidation Reaction on Platinum. Insight from Experiments and Calculations

Using a combination of experimental and computational methods, mainly FTIR and DFT calculations, new insights are provided here in order to better understand the cleavage of the C–C bond taking place during the complete oxidation of ethanol on platinum stepped surfaces. First, new experimental results pointing out that platinum stepped surfaces having (111) terraces promote the C–C bond breaking are presented. Second, it is computationally shown that the special adsorption properties of the atoms in the step are able to promote the C–C scission, provided that no other adsorbed species are present on the step, which is in agreement with the experimental results. In comparison with the (111) terrace, the cleavage of the C–C bond on the step has a significantly lower activation energy, which would provide an explanation for the observed experimental results. Finally, reactivity differences under acidic and alkaline conditions are discussed using the new experimental and theoretical evidence.

VII. Calculations, [1794]

One sheet of paper arranged by columns for the years 1792, 1793, 1794 with currency amounts and final sums below. "Papers & notes of Thomas Adams" written on verso.

Calculations of stone work in new dining halls and chapel, [ca. 1814]

Estimate for $10,189.62 to complete stone work in University Hall. This includes the front basement, end basement, window stools, door ports, and stairs.

[Salary and Treasury calculations and accounts], 1801

Three leaves with handwritten calculations and account information related to faculty salaries, the assignments on delinquents, rents, and repairs. One leaf is inscribed "R. Hallowell Feb. 28 1801" and likely refers to Robert Hallowell (later Gardiner), a member of the Harvard Class of 1801.

[Repairs and occasional expenses calculations, 1801]

Slip of paper with calculations for unidentified "repairs" and "occasional expenses" between 1796 and 1801.

VII. Calculations, [1794]

One sheet of paper arranged by columns for the years 1792, 1793, 1794 with currency amounts and final sums below. "Papers & notes of Thomas Adams" written on verso.